In 1644, with the collapse of Ming Dynasty, Qing Dynasty rose to govern the whole country. At the beginning, Tibet was under the military control of Mongolian Huxut. With the support of the Mongolian military, the Gelupai (Shamanism), founded in the 15th century, has been absolutely superior over the other religious sects. To proceed from the reality of Tibet, Qing government made such decisions: on one hand, they awarded Gu Shihan, the leader of the Mongolian military, as "Zun Xing Wen Yi, Hui Min Gu Shihan" (that's to say, Gu Shihan is of great ability, smart and brave), and allow for his government of Tibet as Han Wang( Han King). On the other hand, the Qing government granted the leader of Shamanism with sublime glory. So Ngawang Lobsang Gyatso, the 5th Dalai, was awarded a golden seal with letters of "Xi Tian Da Shan Zi Zai Fo Suo Ling Tian Xia Shi Jiao Pu Tong Wa, Ci La Da La Da Lai La Ma", and Lobsang Yeshe, the 5th Panchen Lama, as Panchen Lama Erdene. In this way, the title of Dalai and Panchen as well as their position of leading religion has been assured.
The upper ruling group have been in deputes with each other from time to time, which attracted the attention of the government. In 1709, the Qing government put the order that it is inconvenient for La Zhanghan to manage the affairs of Tibet by himself, so they sent Dailangheshou to Tibet to assist La Zhanghan, which is the beginning of Qing's managing the Tibet affairs. In 1718 and 1720, the Qing government sent troops to Tibet twice, forcing out the Zhun Gaer tribe and killing La Zhanghan, which put an end to the Mongolian Huxut's controlling over Tibet and maintain the social order. Later on, in order to strengthen the management, in 1721, the government removed the position of Diba, and apposited 4 Kalon to manage the affairs. In 1727, the Qing government established the Yamen for the commissioners in Tibet, dispatching two ministers to Lhasa to manage the affairs. In 1751, the Qing government set up Kashag as the local government of Tibet. In 1757, the 7th Dalai passed away, so the government dispatched Dimutuketu to regent the affairs in religion and politics, and in the position of Dalai before new one was founded or grownup, it was from then that the regent rules was established. In 1791, the great invasions of Gorkha happened in Tibet, so the 8th Dalai, 7th Panchen and the administers there made a report of that and ask for army to fight against the invaders. Immediately, the government dispatched troops to Tibet, and in the support of the local people, they expelled all the invaders out of there. After that event, the Qing government tightened up the management of military defense and administration. In 1793, 29 articles of Regulations for the Better Governing of Tibet was enacted, which made a specific provision of the local organizations, policy, economy, military, diplomacy and religion, thus fulfilling the ministry. The regulations had been in effect till 1959, before the democratic reformation.