Uncle
Shuichi is very grateful for his uncle for taking him in and taking care of him after his parents moved overseas. To show his gratitude, he worked as his uncle's assistant and learned to be a detective by watching his uncle's example. However, he had no interest in being a detective himself and was simply helping out. While Shuichi feels anxious over being a detective, he does not seem to hold it against his uncle, and they appear quite close.
Parents
Shuichi has a negative relationship with his parents, though he tries to hide it by claiming that he doesn't have any sad story concerning them. His parents are a famous actor and a screenwriter, and considered celebrities by most people, though Shuichi does not view them like that. After they went to live overseas for business, they left Shuichi to live with his uncle, and he appears bitter whenever talking about them though he forces a smile. Shuichi's parents are neglectful and prefer to not be involved with him, and Shuichi has stated that their way of being parents is "hands-off parenting".
Kaede Akamatsu
Shuichi seems to strongly believe in Kaede, reassuring her and telling her that "if it's her, she can do it". His presence appears to put Kaede at ease, due to his status as a detective, although she admits that he seems unreliable. She even attempts to help raise Shuichi's confidence by giving him pep talks.
Shuichi admitted to not having a reason to trust Kaede when murders occur, which disappoints her, although she does learn to accept this since she believes he can solve cases easily if he puts his mind to it.However, this changed when the two began to investigate the school together, as Shuichi came to admire her for her tenacity and determination, putting complete faith in her. He even bowed down to Miu when the two requested her service as an inventor, following suit after Kaede bowed first, which surprises and impresses the pianist.
Shuichi was devastated to find out that Kaede had murdered Rantaro, and desperately demanded to know why Kaede cared for others too much, to the point she committed a murder to save everyone. But his anger faded quickly as he was reminded that Kaede would be executed. He was shown to have attempted to save her, however, this failed as she was already out of his reach, and Shuichi was forced to watch helplessly as Kaede was executed.
Although hurt by Kaede's supposed betrayal, Shuichi still cried over her demise. He imagined her playing the piano after the trial, and was suddenly motivated to keep moving and break out of the school for her.
In chapter 6, when the real case of Rantaro's murder is brought to light, Shuichi is enraged at the injustice Kaede faced, being falsely accused of a crime she didn't commit and therefore was falsely executed. He was later shocked when Tsumugi claimed that Kaede only encouraged him because the mastermind made her like that and that real Kaede would have never said that.
Kaito Momota
Kaito quickly becomes Shuichi's closest companion following Kaede's demise, and they come to share a close bond. After Kaede was executed in the first trial, Kaito states how Shuichi pisses him off the most and immediately punched him in the face, saying that he's angry Shuichi didn't do anything to stand up to Monokuma and that it was disrespectful to Kaede's memory to sit there and do nothing. Kaito backs down when the others criticize him for punching Shuichi, though, and when everyone leaves the trial room, he suggests Shuichi visit Kaede's talent lab. He says that although Monokuma made it, it was filled with things Kaede loved. Taking his leave, Shuichi follows his advice and visits Kaede's lab.
The morning after, he visits Shuichi's dorm to apologize for yelling and punching him and tells him that he's there to take Shuichi to breakfast. It was shown that Kaito visits Shuichi often and invites him to hang out with him, and makes him his "sidekick". They investigate together and help one another, Kaito saying that if Shuichi needs support, he'll always be around to help him. When Shuichi's stuck with clues in the Class Trial or feeling unconfident in his abilities, Kaito helps Shuichi by motivating him and staying on his side. In the original Japanese version, Kaito started to call Shuichi by his first name, while calling him "bro" in the English version, proving that the two shared a close bond.
Shuichi was greatly saddened to discover that Kaito was the one who killed Kokichi in Chapter 5. Kaito told Shuichi that he was, actually, jealous of Shuichi for his deduction abilities. Because of his reasoning, they were able to stay alive, passing many Class Trials. Kaito made him promise not to cry, however, Shuichi had immense difficulty following through on this. When asked by Maki if he was lonely with Kaito gone, Shuichi confirmed this and admits that Kaito is the only reason why he is still alive. He was once again motivated by the death of another friend and was determined to keep moving forward. Many of Shuichi's happy memories during the killing game were shown to involve Kaito, showing that he still remembered him as a close friend and companion.
In general, Shuichi greatly admires Kaito for his honesty and helpfulness, though he does recognize his sillier moments. According to Shuichi, he has never been around someone like Kaito, and he says that his own insecurities and anxiety fade away in his company. He thinks it might be what he has been missing all this time and that "only someone like Kaito could tell him what he needs to hear".
Maki Harukawa
Shuichi and Maki got along well after the events of Chapter 2 after Kaito brought Maki to their training regime. This resulted in the three doing exercises together, although Maki outmatched the two boys at everything they did. Shuichi seemed impressed with Maki's skills, and the three began to meet up nightly to do these exercises. As the two grew closer, Maki began to feel more comfortable around Shuichi, although she still had some trouble trusting others. Despite her cold and rather intimidating demeanor, Shuichi is one of the students who trusts Maki despite her status as an assassin.
Although Shuichi initially only trusted Maki because of Kaito, he grows to genuinely care for and believe in her. In Chapter 3, when Maki confides in him about her not feeling "human", Shuichi assured her that he can relate, as he has his own insecurities about his work as a detective. Because of this, Shuichi strongly supported Kaito's decision to take down Maki's "mask", as he believed he is the only one who can help her open up.
During the events of the virtual world in Chapter 4, Maki did make a point to remind Shuichi that he's a person before he's a detective, which he's touched by, despite her telling him he's more reliable during a murder case than daily life. Nonetheless, it's apparent the two have grown quite close to each other, with her asking if he's okay, making sure if he and Kaito aren't fighting when Shuichi forcibly logged him out to test something.
During Chapter 6, Shuichi and Maki rely on one another as they investigate the school together. Shuichi expressed happiness at the fact that he and Maki have reached the point where he can tell that she's joking. During the last trial, it was partially because of Maki and K1-B0's offer to sacrifice herself that inspired Shuichi to abandon his vote, as he admitted the thought of Maki dying scared him due to what happened to Kaede and Kaito. Shuichi gave Maki courage to end the Killing Game, which resulted in her abandoning her vote as well. The two, along with Himiko, later survived together, escaping to the outside world.
Kokichi Oma
Shuichi didn't trust Kokichi due to his lying and unpredictable actions. However, he occasionally felt like he strangely couldn't sense any malice in Kokichi's smile. In turn, Kokichi appeared to be amused by and in some way fond of Shuichi, having stated that the other boy seems "decently not boring", which is a very rare and notable compliment coming from him. It is implied that Kokichi has a crush on Shuichi. He regularly calls him his "beloved Saihara-chan" in the Japanese version, and occasionally calls him "mister detective" or "mister Ultimate Detective". He also once called Shuichi "Shumai", as a parody to Kaito's "Maki Roll" nickname for Maki. Kokichi enjoys his company, finding him one of the most interesting person in the group and praising him at times. He has also more than once mentioned that he is "constantly thinking about" Shuichi, and claims that he is his favorite who he loves the most. On his whiteboard, it's shown that Kokichi has a more positive, though slightly unclear impression of Shuichi, considering him "trustworthy?". Considering his hatred of boredom, it seems Kokichi is intrigued by Shuichi's development. During the trials, he often does not reveal Shuichi's lies even though he notices them. He occasionally made fun of Shuichi's nervous personality, calling his hat "emo hat" and calling him and Tsumugi a "plain pair".
While he enjoys messing with him, Kokichi appears to feel some care for Shuichi and seems to be unwilling to actually harm him. Throughout his free time events, Kokichi tries to "kill" Shuichi and involves him in many of his selfishness and pranks, though he also seems to make sure Shuichi won't be harmed and seems to just mess with him with words. He also invites him to a tea party and suggests Shuichi could join his organization, so he doesn't have to die. In the last event, Kokichi hurts himself by playing the Knife Game and Shuichi takes care of him in worry. Kokichi is pleased by this and tells Shuichi he won, confusing the detective who answers that he wasn't even playing. Kokichi tells him that games can be won without playing them, foreshadowing the end of the killing game. He then claims he never had an intention to actually kill him. Since he has made Shuichi think about him constantly, he claims he has already "killed" him by "stealing his heart".
In the second class trial's back route, Kokichi notices Shuichi's lie, but decides not to say anything about it, instead, he supports Shuichi to present the evidence of Kirumi's crime since she's the only one who can do it. Shuichi thinks of Kokichi's actions as an "unexpected assist".
Tsumugi Shirogane
The two were in good terms with each other and actually tried to help with each other with the situation. However, in Chapter 6, Shuichi was furious and horrified when he figured out that Tsumugi was the mastermind behind the whole killing game. Despite this, he still wanted her to argue and prove his deduction as incorrect showing that he doesn't consider her any less of a fellow friend or comrade, nor does he wish to condemn her either.
When she acknowledges his claims that she was the one who killed Rantaro and framed Kaede for Rantaro's death, Shuichi seemed to have broken all former ties with her and resolved himself to stop her and end the killing game. Shuichi became noticeably depressed when Tsumugi told him that his memories, feelings, talent, and personality were all fabricated for the sake of the killing game, but he is brought back to his sense when K1-B0 motivated Shuichi to not give up and lose hope.