The temple was first built in the early 7th century. In 616, the first Buddhist stone scripture tablet was made at the temple by a monk named Jingwan. Because there were debates going between Buddhists and Daoists, and Jingwan feared reprisals from Daoists, he decided to carve his scriptures on stone instead of writing them on paper. The work on the stone tablets continued on for more than a thousand years before ending in 1655. In the Sui and early Tang twelve sutras were carved. In the Liao and Jin the Khitan Tripitaka 《契丹大藏經》 was carved and this is the only one of this version of the Chinese Buddhist canon surviving today. Carved on 77,000 wooden blocks the scriptures attract a large number of visitors.  In total, 1122 Buddhist scriptures in 3572 volumes were produced at the temple. In the 1930s, a significant portion of the temple was destroyed. Two bone fragments believed to belong to Gautama Buddha are enshrined at the site. 
There were originally six halls in the temple, arranged from east to west. On both sides of the halls, there was accommodation for guests and dormitories for monks.
- Dan Jixiang and Wang Fengjiang (Eds), 2001. Fang Shan Yu Ju Temple Liao Jin Stone Sutras Preservation Record, No ISBN. In Chinese. 《房山云居寺辽金石经回藏纪实》/单霁翔、王风江（主编）
- Liao Pin and Wu Wen. The Temples of Beijing. Beijing: Foreign Languages Press, 2006.
- http://whc.unesco.org/en/tentativelists/5319/. Retrieved on June 1, 2008.