Tuoba Si was born in 392 after his father Tuoba Gui had founded Northern Wei in 386 but before he had conquered most of rival Later Yan's territory and claimed an imperial title in 399.
His mother was Tuoba Gui's favorite consort, Consort Liu, the daughter of the Xiongnu chief Liu Toujuan.
He was born at the capital Yunzhong (in modern Hohhot, Inner Mongolia.)
Heis Tuoba Gui's oldest son, and his father was said to be so pleased by this late arrival of a son that he declared a general pardon.
(It should be noted that based on Northern Wei's official history, Tuoba Gui would only be twenty-one at this point; this might be further evidence corroborating the alternative version of his life history.)
As Tuoba Si grew, he was said to be a wise and kind young man, whose actions were all in accordance with proper protocol.
In contrast, his oldest younger brother Tuoba Shao was a frivolous and violent young man, and often received punishment from Emperor Daowu.
Tuoba Si tried to correct his brother's behavior by rebukes, but this made Tuoba Shao angry at him.
In 403, Tuoba Gui, by this point Emperor Daowu, created him the Prince of Qi.
In 409, Emperor Daowu is intent on creating Tuoba Si crown prince, but based on the Tuoba tradition that when an heir is decided upon, his mother must be put to death, the emperor forces Consort Liu to commit suicide.
Either before or after he does so, he summons Tuoba Si to explain to him that this tradition is also in accordance with Emperor Wu of Han's rationale to put to death his favorite concubine, Consort Zhao (the mother of Emperor Zhao of Han), to avoid overly great maternal influence on a young emperor.
After Tuoba Si leaves his father's presence, because of the affection that he has for his mother, he mourns greatly.
Hearing this, Emperor Daowu summons him back to the palace—and, because Emperor Daowu, in his late reign, often displays great paranoid and violent tendencies, the new crown prince's attendants suggest that he not go to the palace but hide in the country.
Tuoba Si agrees and flees the capital, Pingcheng, where Emperor Daowu had moved the capital in 398.
Meanwhile, Emperor Daowu, because of the crimes of Tuoba Shaos, had imprisoned Tuoba Shao's mother Consort Helan and planned to execute him.
Consort Helan sends her son a message, asking him to save her.
In response, Tuoba Shao assassinates Emperor Daowu, then tries to take over as emperor, attempting to seize control of the troops.
Tuoba Si, upon hearing this news, returns to Pingcheng but hides himself, while trying to gather supporters gradually.
Tuoba Shao tries to seek him out in order to to kill him, but the imperial guards gradually shift to Tuoba Si's side, and the imperial guards arrest Tuoba Shao and present him to Tuoba Si.
Tuoba Si executes Tuoba Shao, Consort Helan, and Tuoba Shao's associates.
He then takes the throne as Emperor Mingyuan.