Gonchen Monastery was founded by Thang Tong Gyalpo (or Tangton Gyelpo) (1385-1464), a Buddhistyogi and polymath, physician, and treasure finder, renowned for founding of Ache Lhamo, the Tibetan opera, and the numerous iron suspension bridges he constructed throughout the Himalayan region. He is said to have made 108 of them, the most celebrated being the one over the Yarlung Tsangpo near modern Chushul. He is often shown in murals with long white hair and holding some chain links from his bridges.
The monastery was restored in the 1980s and the three inner sanctums are dedicated to Guru Rinpoche (Padmasambhava), Sakyamuni Buddha (Sakya Thukpa) and the future Buddha, Jampa or Maitreya. On the way downhill to the printing press there is a small alley which leads off to the left to the Tangton Gyelpo Chapel (Tangyel Lhakhang).
The main chapel of the monastery is an extensive complex which resulted in it being called the "great monastery". The monastery has a notable design, with striped walls of white, dark red and gray, colors unique to the Sakya sect of Tibetan Buddhism.