65-year-old Tenzin Delek Rinpoche was serving a life sentence in Sichuan province, CNN reported citing Central Tibetan.
Administration, which operates out of the Indian city of Dharamsala.
Tenzin Delek was found guilty of setting off explosions and inciting separation of the state in 2002, died on Sunday.
He was initially sentenced to death but was commuted to life imprisonment on 26 January 2005.
"We are very sad; it's shocking news for us. He has been a very prominent religious teacher. His case has been brought up internationally for years," Tashi Phuntsok, spokesperson for the Central Tibetan Administration, said.