Senku and his adoptive father's relationship was complex but was overall a loving one.
They got along, with Byakuya encouraging him to pursue his goals of science by not hesitating to sell his car in order to give Senku the opportunity to explore his scientific interest. In return, Senku helped Byakuya become an astronaut. Before going into space, a grateful Byakuya promised to bring his son back souvenirs, something that Senku was amused to see prior to the Petrification.
In the thousands of years after the Petrification, Senku discovered that his father created the Ishigami Village and told tales of him in order for the stories to reach Senku after his release.
Although Senku hardly shows affections, he secretly cared for his adoptive father and was sad that while he survived the Petrification, Byakuya died years later. Senku even shed tears at his father's grave however, he was pleased his father held such faith in him to restore the world. Despite not being related biologically, he acknowledges Byakuya as his father, since he raised and supported him.
He appears to think of him from time to time, as he was happy at hearing his voice on a recording. During the time on Treasure Island, he reflected on Byakuya being there with his comrades.
Above even their mutual love of science, discovery, and pushing the limits of humanity's potential, Senku and Byakuya shared a critical trait: their belief in fun being crucial to humanity in all its forms: music, manga, movies, games, literature, and more. The two were always smiling in the midst of a difficult venture and found the thrill of a challenge exhilarating. The ability to find the joy in even crucial tasks where lives were at stake was part of what allowed both of them to withstand the trials and tribulations they faced in their steps towards restoring civilization.
Taiju and Senku have been friends since childhood. In the past, Senku was protected by Taiju from bullies. This led Senku to develop a deep sense of respect and trust towards Taiju, even though he is an airhead.
When Senku was depetrified, he did everything he could to survive, but admitted that he needed Taiju and his endurance to overcome the obstacles to come. Taiju was the first person that Senku revived and he later becomes a major part of Senku's plans to expand the Kingdom of Science, his strength and endurance proving vital to the Power Team.
While the two are pretty much polar opposites in pretty much every way, they are very similar in that they are both very resilient in the face of adversity. Taiju has an unconditional trust in Senku, despite not being able to understand the majority of his friend's plans, but manages to contribute with bouts of insight and his enormous strength of will.
Yuzuriha and Senku are friends through Taiju. Senku knows how deeply Taiju loves Yuzuriha (and vice versa) while respecting his friend's love interest. Prior to the petrification, he was confident that Yuzuriha would accept Taiju's confession.
Once she revived, he wanted her and Taiju to escape from Tsukasa. He is even willing to sacrifice himself to protect her and gives the depetrification formula to Tsusaka  In return, she tended to him and was the one who revived him from Tsukasa's attack. She agreed to his request to act as a spy on Tsukasa.
Following the end of the Stone Wars, she became an official member of the Kingdom. She possesses a genuine ability for tailoring, which is useful for the Kingdom of Science. He also has her use her sewing skills to fix broken petrified humans.
Yuzuriha is one of the few people not put off by Senku's lecture or experimental tests, since she had experience with it.
Kohaku sees Senku as a gentleman, when she watched him defend Yuzuriha and was rather impressed by him. She first sees him sacrificing himself to save Yuzuriha and since that moment, she admitted that she has been very interested in him. She leads him to the Ishigami Village where he meets all the other villagers. She does not trust in Senku at first but, over the course of their adventures, she accepts him and trusts him with very important things, like Ruri's life. Also, she may consider him a very close friend as she is not very offended when Senku calls her a lioness and especially a gorilla, and even admits to him that she finds him physically attractive.
In turn, Senku greatly relies on her due to her physical strength and skill as a fighter. She often helps him in his scientific endeavors by gathering material or lending her physical power. Though he enjoys teasing her by calling her lioness or gorilla (which she hates), he genuinely cares for her as a close ally and friend and trusts her abilities, as shown at Treasure Island, where he has her spy on the tribe by entering into the harem and the two manage to communicate their plans and deliver materials to each other in secret.
Kohaku once kissed Senku, in order to cover from Kirisame, but he was in shock rather than joy. However, she hugged him after he revived her from petrification.
At first, Senku and Chrome had a rivalry. Chrome proclaims himself to be a genius sorcerer and Senku claims to be a scientist. Chrome shows off his skill to impress Senku, Kohaku, Kinro and Ginro, but is completely overwhelmed when Senku reveals that he knows all of his tricks.
Nonetheless, Senku is impressed by all the knowledge that Chrome has learned all by himself. In a way, he reminds Senku of himself. After a small duel between the two, Chrome loses to Senku and is quick to join his Kingdom of Science, being impressed and even fascinated by some of humanity's inventions. They then team up to overcome the challenges towards creating the cure-all for Ruri.
Chrome eventually assists Senku in many ways, including discovering the ore deposit that the Kingdom of Science needs for their campaign.
A twisted mentalist. Originally sent by Tsukasa as a spy, he later defects to work with Senku. Realizing that he can revive science, Gen becomes one of Senku's most trusted retainers to manipulate others and advance Senku's plans. Senku himself has no problems with Gen being a turncoat and becomes close friends with him. As a gesture of good faith, Senku recreates Gen's favorite drink, cola.
The two are both intellectual equals, though Gen is more talented in the science of psychology and the art of manipulation and lacks in most fields of physical scientific knowledge. He assists Senku by manipulating people into following Senku's orders, facilitating cooperation, and helping Senku prepare for the bloodless war against Tsukasa. While Gen initially claims that he joined Senku's army for the benefits, he later admits that he had seen Senku write his liberation date and name on a stone, as he became fascinated with the person who could not only know the year and time they were de-petrified, but also swore to bring back science, telling Senku he already liked him a lot before they met. Gen even goes so far as to have the Ishigami village help him build a telescope for Senku's birthday, something that was greatly appreciated. 
Senku himself greatly trusts Gen with his plans and the two enjoy scheming together, such as tricking Ryusui into buying lots of items, such as clothes and sportswear, so that they would have funds to buy oil from him. Gen is frequently amazed by Senku's inventions, often acting as the straight man to the many amazing scientific developments Senku accomplishes and holds great faith in him. In turn, Senku acknowledges Gen as not being completely devoid of a moral compass, despite Gen claiming to be the most shallow man he'll ever meet.
Suika first meets Senku while he, Chrome and Kohaku are gathering black sand in the nearby river. She wants to help them, as she was often ridiculed and was never of help to others. She immediately becomes attached to Senku after he does not ridicule her for wearing a melon on her head or ask her about it (though Kohaku and Chrome point out that he more than likely didn't care).
He is genuinely impressed by her stealth and ability to hide and gather information, employing her to find out what the villagers like so he could use science to bait them to his side. Later, as thanks, he makes glasses for her when he learns she wears the melon rind to see better (as she is nearsighted and the pinhole effect of wearing the melon helps her to see). He ensures the first thing she sees are sunflowers and she becomes one of his most loyal friends, often helping him gather information and assisting in his labor-intensive work.
He shows a good deal of trust in her abilities along with care for her. When she befriends a pig, she worries Francois will cook it and Senku implicitly asks Francois to allow her to keep the pig as a pet. He similarly trusts her to help bring the lab to him when she was the only one not petrified by the Treasure Island tribe who boarded and took the items of the Perseus.
Senku constantly works with Kaseki in restoring science and making weapons and materials. Kaseki does not trust Senku at first, but the two form a bond over their love of building items and vehicles. The old crafter even admitted things got interesting when Senku came to the village.
When Kaseki and the others are petrified, Senku plans to revive Kaseki first, but is forced to change his plans after Kaseki is thrown into the ocean. Senku later revives Kaseki twice, so that he can help out and to free him from the prison of suspension.
The child of the owner of Nanami Conglomerate. Despite hearing of his twisted personality by Minami, Senku revives him and is impressed by his accurate description of the temperature.
When seeing Ryusui's entitled nature, Senku and Gen tag team to outwit the sailor, much to Ryusui's shock. Together, they team up to search Sagara Oil Fields that have been discovered by Kohaku and prepare for a journey in a search of the source of petrification.
Senku finds Ryusui amusing, since he has rebuilt currency and his advanced sailor knowledge. Ryusui also finds Senku to be more devious than him, showing he acknowledges his intellect.
There appears to be mutual respect between them, as Senku compliments his skills. Ryusui also mentions that had they met in the pre-petrification world, Ryusui would have hired Senku for his company.
When Ryūsui is petrified twice, Senku is the one who releases him. He also joined the others in adorning war pain (in reminiscent of his scars) to honor Senku, showing loyalty to him.
A former SDF Navy member who served as a submarine operator.
Although initially enemies, due to their opposing Empires. Ukyo joins Senku after learning he and Yuzuriha are repairing the broken petrified humans.
He becomes one of the vital assets for the Kingdom of Science due to his perk of superhuman hearing. Ukyo joins Senku at being one of the Five Wise Generals.
Originally, Senku is regarded as an outsider, but over time, they have grown to care for him. He is shocked that the village was named after him and their stories were passed down by his father Byakuya Ishigami to reach him in the future.
After becoming chief and curing Ruri, the village has come to accept him and are amazed by his scientific knowledge and the inventions that he has made to benefit them, such as giving Suika and Kinro glasses, building swords to combat the Tsukasa Empire, treating them to cotton candy, and other things. Kokuyo even declared he made the right decision on making Senku leader of the village.
Originally, Senku was regarded as an enemy, due to the conflict between him and Tsukasa. However, they have grown to respect him, since he defeated Tsukasa and the Kingdoms have aligned.
As all the members of Tsukasa Empire were modern timers, they are all amazed by his scientific inventions that he has made to benefit them, such as promising Nikki the restoration of music, giving Minami a camera, and Yo a gun.
Since his depetrification, Senku was always wary of Tsukasa and his goals. Because he is too strong, Senku has no other choice but to consider the possibility of Tsukasa and him not sharing the same principles. Tsukasa, however, deeply respects Senku and asks him to abandon science so that he doesn't have to kill him. Senku on the other hand, shares Taiju's opinion that while Tsukasa is inherently a good person, he is undeniably a murderer which needs to be stopped.
Tsukasa shares his regrets of not having talked to Senku 3700 years ago, saying that he may have become his very first friend, to which Senku replies "probably". The two remain enemies, as Tsukasa's troops frequently try and fail to destroy Ishigami village. However, Senku manages to order a ceasefire with Tsukasa upon revealing he could not only help de-petrify Tsukasa's sister, but also cure her of her brain dead vegetative state. When he does so, Tsukasa is grateful and promises not to harm Senku's group again. He even goes so far as to protect him from Hyoga's attack and trusts in Senku's promise to save him and cryogenically freeze him until he can.
Despite their ideological differences, Tsukasa and Senku respect one another for their intelligence and strength of will.
Hyoga and Senku first meet as Senku manages to create Japanese katanas for the Kingdom of Science. Senku bravely asks Hyoga to tell Tsukasa that he is still alive, thus invalidating Gen's earlier claims. After the battle to claim the Miracle Cave ends in a truce, in exchange for reviving Mirai, Hyoga betrays Tsukasa by stabbing him in his lungs, with Senku following soon after. Thanks to Tsukasa and Senku's joint effort, Hyoga is finally defeated and has been imprisoned on the Perseus.
Later, during the attack of the Petrification Kingdom, Hyoga is revived as Senku's last-ditch effort. In the end, Hyoga decides to help Senku in battling Mozu, and trusted him enough to modify his spear, which allows him to defeat Mozu.
During the voyage to America, Senku decided to free Hyoga while he was still petrified because of Ibara. Senku was concerned about a potential hazard Hyoga may pose, giving Tsukasa the right to handle him. After he was freed, Senku gave him the option to join the Kingdom and Hyoga accepted after he was allowed to revive Mozu and Homura.
He believes he can turn her over to their side despite her strong loyalty to Hyoga. He gives her cotton candy, claiming that he wants to sweeten her up, though Ruri suggests it is actually because she is a lonely girl in enemy territory and he wants to comfort her. Senku uses the blue jewel powder to track her. When she and Hyoga are captured, he keeps the both of them as prisoners rather than kill them.
When they set out on a voyage, to ensure they don't attack the village while he and the main team are gone and in case he needs extra muscle, he forcibly brings her and Hyoga along.
During the voyage to America, Senku allowed Hyoga to revive Homura and she became the navigator to the Perseus.
Kirisame petrified many of Senku's allies on the Perseus.
She allies with Senku after Ibara's defeat.
Mozu initially is about to kill Senku and the Kingdom of Science members after Kirisame petrifies Ginro and Kohaku. However, thanks to Gen using his psychological abilities, they temporarily form a truce to kill Ibara instead and claim Medusa. Mozu quickly betrays the Kingdom of Science after Ibara manages to find out about Senku's plan.
To combat this problem, Senku de-petrifies Hyoga and has him battle Mozu.
During the voyage to America, Senku allowed Hyoga to revive Mozu and he became one of the warriors to the team.
Whyman is the nickname given to a mysterious individual who they received a Morse code message from. Senku believes them to be the individual responsible for the petrification incident, or at least related to it somehow. One of the reasons Senku has built the Perseus is to find out who Whyman is.
Ibara is the former leader of the Petrification Kingdom and formerly, the one who held Medusa, the source of Petrification. He petrified many of Senku's allies. With help from Ryusui, Senku petrified Ibara.