A (seemingly) normal sibling relationship, Shido and Kotori have been living together under the same household for a long time, and are very close despite the two not being related by blood. Shido deeply cares about Kotori (as a big brother) to the point that, he believed a fake promise made by Kotori which is no matter what happens, even if there's a spacequake, she will wait for him at the family restaurant. Five years prior to the present, Shido gave Kotori a pair of black ribbons as a birthday present. Knowing how much of a crybaby Kotori was, Shido wanted to, in his own way, help his sister grow emotionally, telling her that, so long as she wore the black ribbons, she would become her "strong self".
This would come to somewhat backfire on Shido, as Kotori developed a strong, cynical-like personality while wearing her black ribbons, to go along with her position as commander of Ratatoskr. Despite usually being put off by Kotori's bossy attitude while in "commando mode", and her often questionable advice to him during matters concerning the Spirits, Shido still loves his little sister very much.
Shido shares an especially close bond with Tohka that goes beyond the level of mere friendship. He was the one who gave Tohka her name, based on the day of their first meeting, April 10th. Shido cares very deeply for Tohka, as shown on many occasions, always going out of his way to make her happy and teach her the ways of the world. In fact, his feelings of caring towards Tohka are so strong that, when she was captured by DEM, Shido prioritized saving her above everything else, despite the grave risks involved and the enormity of the odds stacked against him.
Later on, as Shido was about to be killed by Ellen right before Tohka's very eyes, she fell into deep despair and unleashed her Inverse form, going on a rampage that almost cost Shido his life. However, even when faced with Tohka's berserk state, Shido still refused to give up on saving her, ultimately bringing Tohka back to her senses with a kiss; further emphasizing the deep feelings of trust and affection between the two.
Shido considers Origami to be a friend. It is unclear how he feels for her despite her "romantic" attempts. Whenever Spirits are involved, their views tend to cross against each other as Origami despises all Spirits and tries kill them, while Shido wants to try to save them, making his overall relationship with Origami complicated at best.
Shido treats Yoshino like a big brother treating a younger sister.
The first time Shido met Kurumi, she immediately revealed herself to be a Spirit and attracted his attention. During their first date, he learned she was also the first Spirit he'd ever dealt with who was actively on the offensive. After witnessing Tokisaki kill someone mercilessly, Shido was left horrified and conflicted, unable to think of what to do until Tohka explained to him that in the end any Spirit, like her, could've become like Kurumi if they had been left alone. He thus resolves to save her, despite being terrified of her and knowing that she intends to eat him. Later on, despite his wariness of her, Shido was fully willing to team up with Kurumi in order to save Tohka from DEM.
To date, she is the only Spirit he has failed to seal, however, she has indeed fallen for him, arguably before he even started to date her, and is something of a Yandere towards him. She is also very teasing, especially after she witnesses Shido having to dress up as a girl to deal with the Spirit, Miku, and openly jokes about it, much to his dismay.
Shido considers the Yamai sisters as close friends.
At first, Miku hated Shido, but only because of his gender, as she hates men in general due to an event that happened to her in the past. Despite this, Shido still cares for her and is willing to help Miku overcome her hate for men, even going as far as crossdressing in order to just be able to speak to her. Shido also did the dangerous act of stopping her berserk state, and also protected her from several grave assaults. In the end, Miku overcame her trauma and her feelings toward Shido changed. Later on, Miku declared Shido as her boyfriend, calls him "darling", and shows her affection toward Shido without hesitation, much to Shido's chagrin.
Shido had a rough beginning with Natsumi, while their date was originally going smoothly, Natsumi turned hostile when she believed he discovered her true form, so hostile she tried to ruin his reputation, erase him, and erase all of his friends in a twisted game. Later, after he saves her from Ellen and tries to convince her that her true form is already cute without her having to hide it, she gradually opens up to him. She has shown some guilt over what she put him through, however, when he remembers being nearly killed by being shot, frozen, eaten, incinerated, blown away or attacked by a huge mob, he considers her actions to be on the level of a mere childish prank. Shido now treats Natsumi as one of his friends and, in a somewhat Tsundere manner, she was willing to help him despite her weakened condition when a satellite was dropped on the city.
Friends, acquaintances, and/or classmates, depending on which one he talks to. But overall, he usually has a mundane or normal relationship with any of his classmates. After Tohka and Origami began competing over Shido, however, many of his male classmates became very jealous of him.