In 643, when Emperor Taizong commissioned the Portraits at Lingyan Pavilion to commemorate the 24 great contributors to Tang rule, Li Shiji's was one of the portraits commissioned. In spring of that year, when Emperor Taizong's son Li You () the Prince of Qi, angry at his secretary general Quan Wanji (), killed Quan and then declared a rebellion, Emperor Taizong sent Li Shiji to attack Li You, although even before Li Shiji's forces arrived, Li You's subordinates captured him. Subsequently, in summer 643, when Li Chengqian the Crown Prince, was revealed to have plotted to overthrow Emperor Taizong, as he was fearful that Emperor Taizong would replace him with his brother Li Tai the Prince of Wei, Emperor Taizong had Li Shiji, along with other key officials Zhangsun Wuji, Fang Xuanling, Xiao Yu, as well as officials in charge of the supreme court, the legislative bureau, and the examination bureau, investigate. They confirmed Li Chengqian's guilt. Emperor Taizong thus deposed Li Chengqian and, believing that Li Tai's machinations were responsible for Li Chengqian's downfall, also demoted Li Tai and exiled them both, creating Li Zhi crown prince instead. Li Shiji was given the additional title as the new crown prince's head of household, and was also given a newly created title of "Tong Zhongshu Menxia Sanpin" (), which title designated him as a chancellor "de facto".