This temple was established by Taizong(r. 650-684), second emperor of the Tang Dynasty, to commemorate the soldiers who died during his failed invasion of Koryo (present-day Korea). The original name of the temple was Minzhongsi. The temple burned down in 882 , and was not rebuilt until the Five Dynasties period (907-960), at which point it became a nunnery. In 1173, Emperor Shizong of Jin had chose this location for examinations fo candidates for the Daoist nuns' orders.
The temple was renovated in 1437, and its name was changed to Chongfusi. It received its present name after it was renovated in 1734. Ordinations were held here in 1921. Notable ordinands included Fafang and Fazun.
After 1956, this temple became the headquarters of the newly-established Buddhist Academy of China, which remains the central Buddhist seminary in China. In May 1980, the East and West halls were converted into the Chinese Buddhist Library and Archives, which houses materials related to Buddhism that are written in many different languages.