Since Tibet formally came under the control of the Yuan court in the mid-13th century, China has seen changes of dynasty and many changeovers in the central authority, but Tibet has always remained under the Chinese Central Government's jurisdiction. During the mid-14th century the Sagya government gradually declined.The Pagmo Gagyu Sect headed by Qamqoi Gyaincain came to power, following the system of temporal and religious administration. Yuan rulers accepted the fact and gave Qamqoi Gyaincain the title Grand Minister of Education. With the overthrow of the Yuan and the founding of the Ming Dynasty :in 1368, a policy whereby titles were widely conferred was put into effect. The head of any religious sects who could claim local political power was given an honorary title such as Prince, Prince of Dharma or Abhisecana State Tutor (Abhisecana being a Buddhist ceremony wherein a student's initiation is acknowledged by his teacher sprinkling water on his head). Succession to the throne was subject to approval by the Chinese emperor who would dispatch officials to deliver certificate acknowledging the title. During this time, the Gelug (Yellow) Sect, which recognized two great Living Buddhas, the Dalai Lama and the Panchen Lama, was gaining in prominence. The 3rd Dalai Lama Soinam Gyatso paid tributes to the Ming court and in return was given the title of Dorje Chang Vajra Holder. The Ming government followed Yuan Dynasty practices regards Tibet. It established the U-Tsang and the Gargain garrison command headquarters and the Olisi Military-Civil Governor's Office respectively to manage the military and political affairs in the Central and Western Tibet, Qamdo and Ngari. During this time, the Tibetan government established thedzongponsystem in parts of Tibet. The administrative heads of eachdzong(an administrative unit about the size of a county) were recognized by the Ming court asdzongpon(county magistrate).

In 1644, the Qing Dynasty overthrew the Ming. The new central power increased control over Tibet, bringing increased systemization and an expanded legal framework. Qing Emperor Shunzhi on several occasions invited the 5th Dalai Lama to Beijing, and in 1652 he did so. In 1653 the emperor gave the Dalai Lama a gold-leaf certificate of appointment and gold seal of authority formally recognizing his status as the Dalai Lama. In 1713 Emperor Kangxi similarly honored the 5th Panchen Lama Lobsang Yeshe formally recognizing him as Panchen Erdeni. Beginning around this time the Dalai Lama based in Lhasa ruled over the greater part of Tibet and the Panchen Lama based in Xigaze ruled over the remainder.In 1727 the Qing court appointed a Resident Commissioner (Amban) as a Central Government representative in Tibet to oversee Tibet's administrative affairs. Tibet's borders with Sichuan, Yunnan and Qinghai were formally surveyed and fixed at this time. In 1721 the Qing Central Government established the Galoon (Ministers of Council) system in Tibet. In 1750 the Tibetan administrative system was reformulated and the icommandery princei system was eliminated. The Tibetan local government (Gaxag) was founded with the Amban and the Dalai Lama together handling Tibetan affairs. In 1793 the Qing government issued the famous 29-Article Ordinance for the More Efficient Governing of Tibet, dealing with the authority of the Amban, the reincarnation of the Dalai Lama, the Panchen Lama and other important Living Buddhas, frontier defence, relations with the outside world, finance and tax revenues, minting and administration of currency, and the support and administration of monasteries. The basic principles formulated in the 29-Article Ordinance remained the standard for the administrative and legal systems in Tibet for more than the next hundred years.

The Revolution of 1911 which toppled the Qing Dynasty led to the founding of the Republic of China, a multi-ethnic, unified country where peoples of the Han, Manchu, Mongolian, Hui, Tibetan and other ethnic groups lived harmoniously. The Central Government continued jurisdiction over Tibet as it had in the three previous dynasties. In 1912 the Bureau for the Mongolian and Tibetan Affairs (in 1914 renamed the Council for the Mongolian and Tibetan Affairs) was set up chiefly to manage Tibetan affairs and a resident official dispatched to Tibet. The Nanjing Nationalist Government came to power in 1927 and two years later it set up the Commission for the Mongolian and Tibetan Affairs to oversee administration of the areas inhabited by Tibetans, Mongolians and other ethnic minorities. In 1940 the Nationalist Government set up the Lhasa Office of the Commission for the Mongolian and Tibetan Affairs in Lhasa to function as the Central Government's standing body in Tibet. The Tibetan government frequently sent officials to participate in the Republic's National Congress. The Republic suffered from incessant foreign aggression and frequent internal disturbances. But despite the fragility of the Central Government the Dalai and Panchen lamas continued to accept its official recognition of their positions, receiving legal status in their political and religious roles in Tibet. The 14th Dalai Lama Dainzin Gyamco came to power in Tibet with the approval of the president of the Nationalist Government.