元朝(1271-1368年)时期，中央设置总制院(后改为宣政院)，在西藏地区设立宣慰使司都元帅府，中央直接管理西藏军政事务。元朝派军驻扎西藏，在宣慰使司下设13个万户府、千户所等机构。元朝在西藏还设立大小驿站，通往大都；派官员入藏进行三次户口清查。元世祖忽必烈任命萨迦派八思巴为帝师。后来噶举派取代萨迦派的地位，元顺帝时封其首领强曲坚赞为“大司徒”。

　　明朝(1368-1644年)时期，基本沿袭了元朝对西藏地方的管理制度。在政治上，实施多封众建，给西藏各地宗教领袖封以“法王”“灌顶国师”等名号；在经济上，发展茶马互市，促进西藏与其他地区的贸易和往来；在机构设置上，在今西藏中部和东部设立“乌斯藏行都指挥使司”“朵甘行都指挥使司”，隶属于陕西行都指挥使司，在西部设立“俄力思军民元帅府”。

In the Yuan Dynasty (1271-1368), the central government established the Supreme Control Commission of Buddhism (later renamed the Commission for Buddhist and Tibetan Affairs), and set up in Tibet the Chief Military Command under the Pacification Commissioner's Office to directly manage the region's political and military affairs. The Yuan court stationed troops in Tibet, and set up 13 organs, including the 10,000-man Brigades and 1,000-man Battalions under the Pacification Commissioner's Office. The Yuan court set up courier stations on the road leading from Tibet to the capital city of Dadu, and sent officials to Tibet three times to conduct census. Emperor Shizu of the Yuan Dynasty, Kublai Khan, appointed Phagpa from the Sakya School of Tibetan Buddhism as Imperial Preceptor. Later, when the Kagyu School replaced the Sakya School, Emperor Shundi appointed the Kagyu leader Changchub Gyaltsen "Ta Situ."

The Ming Dynasty (1368-1644) generally followed the Yuan administrative system for Tibet. Politically, the Ming court implemented a policy of multiple enfeoffment, conferring the titles "Prince of Dharma" and "Imperial Empowerments Master" upon religious leaders in Tibet; economically, it promoted the tea-horse trade to increase Tibet's trade and exchanges with other regions; in terms of organizational structure, it established the u-Tsang Regional Military Commission in today's central Tibet and the Do-kham Regional Military Commission in eastern Tibet, both subordinated to Shaanxi Regional Military Commission, and the Ngari Commanding Tribal Office in western Tibet.