Natsuo feels a strong animosity towards his father, for his negligence towards him and his siblings who did not inherit a powerful Quirk to surpass All Might, as well as for being the reason that his mother ended up hospitalized, and considering him the principal responsible for the death of his brother Toya. Natsuo mentions that he hardly remembers his father, which means that Enji did not do much in raising him. This aversion does not allow him to spend much time in the same room as his father.
After Endeavor defeated Hood, while getting a scar on his face similar to Shoto's as a result. Enji returned home, finding his children eating dinner. Natsuo, along with Shoto, tensely glared at him and only spoke up about his new scar. When Natsuo moved to leave, Enji stopped him and told his son to speak up. With this, the latter angrily confronted him on everything he's done, even saying he's incapable of change and blames him for the distance between him and Shoto, as well as what happened to Toya. Enji simply remained silent at the rant before calmly stating he will face his past to atone. Natsuo was surprised by this statement and left. Enji spoke with Fuyumi and stated he chose the wrong words with Natsuo.
Months later, Fuyumi organizes a dinner in which he invites Natsuo to eat with his father, brothers and Shoto's classmates, Izuku and Katsuki. Out of respect for his sister Natsuo accepts. The tension with Enji remains high, as he is the first to leave. Shortly after leaving dinner, Natsuo is captured by Ending, a criminal who wants Endeavor to kill him. By putting his child in danger, Endeavor freezes because he's traumatized by the look on Natsuo's face. Fortunately, Shoto, Izuku and Katsuki manage to defeat Ending and rescue Natsuo.
Endeavor embraces Natsuo grateful that his son's life is safe. As Natsuo breaks free of Endeavor's grasp, Endeavor confessed that he is regretful for what he did to the family due his negligence and the damage caused accordingly. Natsuo tells his father he doesn't care and declares he is unable to forgive him, unlike his mother, Shoto, and Fuyumi. Endeavor responds that he sees Natsuo as kind enough and states that it's okay if Natsuo doesn’t forgive him because he's not looking for it, he just wants to atone for his mistakes.
Crying, Natsuo questions why he has to be the only one to try and proactively change and what exactly will Endeavor do to atone. Later, Enji confesses he will have a new house for him, Fuyumi and their mother, as he realizes that the only thing he can do to help his family to take himself out of the equation.
Along with Fuyumi and Shoto, Natsuo usually visits Rei in the hospital. Like his other siblings, Natsuo has a positive relationship with his mother, with Natsuo complimenting his mother's healthy complexion and recommending her to get a phone to better keep in contact with Shoto.
Natsuo loves his mother very much, and he cares for her, and that she has ended up in a hospital for several years is one of the reasons for Natsuo resentment towards his father, whom he believes he never apologized for what he did. However, Rei reveals that that is not true, because his father did come and visits many times but not face to face. From this conversation, Natsuo understands that his mother has forgiven his father. He respects her decision even if he doesn't share the same will.
In Fuyumi's words, Natsuo had an excellent relationship with their older brother Toya when they were kids, and they always played together. Toya's death, which happened shortly after his mother went away, greatly affected Natsuo, which caused him to greatly resent his father, whom he considers to be primarily responsible for what happened to Toya.
Natsuo knew about the harsh training the Toya was subjected by his father, since he told him everything and still can't forgive his father for it.
Natsuo has a good relationship with his older sister Fuyumi, and as with Toya, they usually played together as kids. The pair still get along in their older years, with Fuyumi regularly teasing him in their visit to their mother, to his dismay.
However, unlike him, Fuyumi is able to look past their father's faults. He knows that she is trying so hard to fix the family that Endeavor broke, and that everyone can live together as a real and normal family. For this reason, for Fuyumi's sake, he is willing to begrudgingly participate in which his father is present, to respect the feelings of his sister, although this inevitably generates tension and Natsuo usually leaves to avoid more problems.
She also expressed concern for him after he was attacked by a villain, which he assured his frantic sister.
As a child, Natsuo could barely interact with with his younger brother because their father avoided any interaction between them since he had to train Shoto to make him stronger and surpass All Might. Once they grow up, they begin to interact more frequently, and in general their relationship is quite good, due to their shared resentment of their father.
During the Pro Hero Arc, he spent time with his sister and brother until their father returned home. Natsuo soon told off Endeavor and blaming him for his previous treatment, making him unable to know much of his brother. A surprised Shoto noted that he never saw his brother become as emotional as he did. He also seemed to sympathize with his Natsuo's point.
Months later, after a dinner at the Todoroki Abode, Shoto was concerned for him after he was attacked by a villain. With help from Izuku and Katsuki, Shoto secured his brother's safety and defeated Ending. After the attack, Natsuo thanked him and his friends for saving him.
Natsuo meets Shoto's classmates when they were invited to have dinner with them at Todoroki Abode. During dinner there was hardly any interaction between them since Natsuo did not stay long in the place.
This changes after they, along with his brother, rescued him from Ending. Natsuo is grateful that he will save his life, especially to Katsuki who was the one who rescued him directly, asking him what his hero name is, although Katsuki doesn't tell him.