Under his leadership, the temple started opening schools outside China and formed a travelling troupe of monks who performed Shaolin kung fu shows - the temple's signature style of martial arts.
News of Mr Shi being investigated was the most read topic on Weibo on Monday morning. The last post on his own Weibo account, which has more than 880,000 followers and had been updated daily with Buddhist teachings, is dated 24 July.
Mr Shi also came under scrutiny in 2015 for allegedly having sexual relations with women and embezzling temple funds. He also allegedly received expensive gifts from companies and local governments, including a Volkswagen SUV and a robe with gold thread.
He was investigated at the time for embezzlement and fathering several children, but was later cleared of the charges.
In an interview with BBC Chinese in 2015, Mr Shi was asked about the allegations of corruption and affairs with women.
"If there were a problem, it would have surfaced long ago," he said at the time.
Shaolin Temple also came under fire in 2015 over a plan to build a nearly $300m temple complex which also included a hotel, a kung fu school and a golf course.
The name "Shaolin" has gained prominence in pop culture over the years, including being the title of a 1982 film starring Jet Li. The temple is referenced in songs by American hip-hop group Wu-Tang Clan and inspired a spinoff of the video game Mortal Kombat.
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