The monestary was established in 1416 by Tsong Khapa's disciple Jamyang Qoigyi, who was versed in both Esoteric and Exotoric Buddhism and became the first Kampo there. With the support of plutocrats, it developed as the richest monastery of Gelugpa and became the mother temple of Dalai Lamas. In 1546, the third Dalai was welcomed as the first Living Buddha into the monastery. At the invitation of Mongolia's king, he went to Qinghai Province to preach. He was dignified with the title 'the third Dalai Lama' the first and second Dalai were entitled, too. It is the very place that the second, third, and the fourth Dalai Lama held the Sitting-in-Bed Ceremony, as well as the residence of the fifth Dalai before his nomination by the government of the Qing Dynasty (1644 - 1911).

The ground of the monastery is organized on the caves and temples for Jamyang Qoigyi, together with two magnificent white pagodas. The buildings of the monastery are centered on these pagodas, The major buildings are Ganden Potrang, Coqen Hall, the four Zhacangs (or Tantric colleges), and Kamcuns.

The Ganden Potrang, in the southwest corner of the monastery, was built under the supervision of the second Dalai Lama Gendun Gyaco around the year of 1530. It became the residence of the second, third, fourth, and the fifth Dalai Lamas. After the fifth Dalai Lama moved to the Potala Palace, it was served as the meeting place for the local regime for both politics and religion.