Shido is Kotori's adopted older brother. Her deep love and care for her brother has been shown many times. However, she treats her brother lowly when she is in commander mode, but clings to him heavily when in little sister mode.
Kotori developed her commander mode persona when Shido gave her black ribbons as a birthday present, and made her promise to be strong when wearing them, since without them she proved to be quite a crybaby. However, when she is wearing her white ribbons or no ribbons at all, she returns to her persona as his younger sister, which proves to be Kotori's true self. A lot of Shido's peers actually find it strange how close they are. According to the Fraxinus' machines, her affection points for Shido neither rose nor fell during their date to seal her Spirit powers: because the said points were already maxed out the entire time.
Kotori can be considered a tsundere towards her older brother, often teasing him and even acting a little sadistic towards him while in commander mode. Despite her usually blunt and harsh attitude, however, Kotori's feelings for Shido run deep, and have been shown numerous times to go beyond the boundary of sibling love, to the point of being romantic.
The most reliable person that Kotori depends on when she needs to ask for advice. It has been stated several times that she is Kotori's best friend.
Kotori treats Kyouhei poorly due to his antics and small obsession with her, leading to her ignoring him most of the time. However, she trusted him to command <Fraxinus> when she was not present.
Kotori and Mana are both rivals at being little sisters to Shido. However, after Mana defected from DEM, and stopped a hypnotized Kotori from killing Shido, their relationship has greatly improved to the point that Kotori is begging Mana to get treatment for her body. As such, Kotori has now come to see Mana as a part of her family as well.
She treats them all fairly as their commander. It's noted by her that she sees most of her crew as a family, and has memorized the names and ranks of every single member of it, even the ones she has never had any direct contact with whatsoever.