The Qing Dynasty established the capital in Beijing in 1644, and united China. It exercised the sovereignty over Tibet according to the practice in history. The Qing rulers decreed that those in Tibet granted official titles by the Ming court might retain their official position so long as they turned over their official seals and applied for new ones from the Qing court. In 1652, the 5th Dalai Lama was summoned to Beijing for an audience with Emperor Shunzhi; he received his official title from the Qing court the following year. The honorific title of the Dalai Lama was finally officially determined and the following generations of the Dalai Lama all had to seek Central Government certificates of appointment and seal of authority for their rule in Tibet.

Based on the experience gained by the Yuan and Ming dynasties in rule over Tibet, the Qing court did the following: Stationing High Commissioners in Tibet; Readjusting the temporal and religious administration system in Tibet; Granting honorific titles to the Dalai Lama and the Panchen Erdeni; Establishing the principles such as foreign affairs and border defense of Tibet being the prerogative of the Central Government.