Shinji is Sakura's brother but no related by blood and he has no talent at magic, only knowledge.
Shinji was born without any capacity for sorcery as a result of the Matou family's thinning bloodline to produce natural-born magi, even when his father Byakuya had married a woman with an "inheritor" sorcery trait. Wanting an heir capable of producing magic, Zouken would adopt Sakura Tohsaka into the family. At first, Shinji was accepting of Sakura, despite his selfish nature leading him to deny it on the surface as he would regularly tease her. But after Sakura was infused with Zouken's worms, Byakuya would come to neglect and abandon Shinji due to the pressure of being under Zouken's influence. As a result, Shinji became increasingly angry and abusive with Sakura. Out of pity and guilt, Sakura would take the abuse and Shinji took this as the girl submitting to him.
When his father died, Shinji's feelings of loneliness, due to Sakura getting attention from Zouken for training, enraged him to the point where he started to violently rape her of her own volition. Desiring to become the heir of the Matou family, Shinji is able to persuade Zouken into allowing him to become Rider's Master in the 5th Holy Grail War by having Sakura give up her right to be a Master in the Grail War due to her lack of desire to fight.
Shinji has the curly blue hair and grey eyes that his father has. He stands at roughly 66 inches (167 cm) tall and is seen wearing either his school uniform while attending classes or wearing a white and black jacket, black shirt and blue jeans for casual clothes.
Shinji is a haughty and selfish young man, known to have a short temper. He is also a violent, manipulative and controlling person as a result of the neglect he received from Byakuya and Zouken, driving him to take his anger out on his adoptive sister, Sakura. Having the strong desire to be the heir or the Matou clan, Shinji has a strong hatred for rejection due to his desire to be acknowledged positively for his efforts.
Shinji and Rider serve as the first major threat that Shiro and Saber confront when they become aware of Rider making use of her Bloodfort Andromeda Noble Phantasm to drain the life force of the student body in the school to supply her mana reserves. He tries to convince Shiro and Rin to partner up with him, but to no avail. Shinji then tries to have Rider kill Shiro at the school, before Saber comes to his rescue and the two manage to force the two to flee. The two Master/ Servant pairings then have a final confrontation atop the buildings of Fuyuki where Saber manages to defeat Rider using Excalibur. With Rider defeated, Shinji tries to flee yet is killed by Ilya and Berserker.
Following Rider's defeat to Saber and Shirou, Shinji tracks down Kotomine Kirei, who lends him Gilgamesh as his Servant. He is unaware that Gilgamesh is manipulating him for his personal gain as the King of Heroes has him go to Ilya's location, so she can be killed. Gilgamesh would later turn Shinji's body into a vessel for the Holy Grail by implanting Ilya's heart into him. After Gilgamesh's defeat, Shinji is rescued by Rin and hospitalized. According to Shiro, Shinji abandoned his selfish personality and became more nicer to Sakura.
Heaven's Feel expands on exploring the relations between Shinji and Sakura. After losing control of Rider, Shinji is berated by Zouken for his failure and worthlessness as a Matou family member. Infuriated, Shinji begs for another chance as he becomes far more violent and merciless in his abuse towards Sakura.
Knowing of Sakura's feelings for Shiro, Shinji tries to take her home by force, yet is stopped by Shiro. The following day, Sakura is abducted by Rider when Shinji regains control of the latter with another Book of False Attendant. Shiro is forced by Shinji to come to the school alone and take on Rider. Weakened due to Shinji's lack of mana capacity and unwilling to follow his order, Rider gets forced by Shinji to kill Shiro. But following a scream by Sakura, the book is destroyed and Shinji once again loses control of Rider.
Having a breakdown, Shinji tries to force Sakura to aid him in killing Rin and Shiro, but to no avail. Shinji's breakdown then worsens when he recalls his painful past and believes, in his delusional state, that Shiro and Sakura are responsible for his suffering. When Sakura arrives at the Matou household to find Zouken, Shinji attempts to rape Sakura and have her submit to him by threatening to tell Shiro about having her being raped the past three years. This leads Sakura to kill Shinji and make her realize that she was "the shadow" under Zouken's control, leading her to become Dark Sakura.
Shinji possesses no actual ability as a magus due to the thinning bloodline of his family. As a result, he would normally be incapable of being a Master for the Holy Grail War. However with the Book of False Attendant created from one of Sakura's Command Spells, Shinji attains a temporary Command Spell that grants him control of Rider, who was summoned as Sakura's Servant. However, the book's effects are not as powerful as a real Command Spell and it can burn away when either Rider is destroyed or if it is used beyond its limits. The book also appeared to allow Shinji to use a limited degree of magic as it could fire shadows at its foes in the Fate route. However, this magic was weak enough where even Shirou could cut them away using a reinforced broom.