In 1235, Mongolia attacked the Southern Song Dynasty on a large scale. The great-grandson of Genghis Khan, called Godan, was in charge of directing the forces on the western route. In order to tighten the rule over Xixia and the Tibetan-inhabited areas in Gansu and Qinghai and guarantee the security of Mongolian forces when they made an expedition southward to Sichuan, he decided to carry out a military action on Tibet so as to being the Tibetan-inhabited area under the control of the Mongol Empire. He sent General Dorta Nambo to lead cavalry deep into Tibet. Godan realized that the local religious forces should be utilized to unify Tibet. He found out that the Sagya had the greatest influence at that time and its abbot Konggar Gyaincain enjoyed the highest prestige among the sects in Tibet. Hence, Godan invited him to meet him in Liangzhou (present-day Wuwei in Gansu).

In 1246, Konggar Gyaincain, on behalf of the heads of monks in Tibet, went to Liangzhou to meet the Yuan prince Godan with his two nephews (Pagba and Chagna Dorje). They negotiated the conditions for Tibet to pledge allegiance to Mongolia. Godan granted the power of governing 13 Wanhu (a kind of social administrative unit or a political unit governed by a tribal chief) in Tibet. Konggar Gyaincain later sent a letter to the heads of monks in Tibetan-inhabited areas to explain that it was the general trend for Tibet to pledge allegiance to Mongolia by enumerating the various facts; the heads of monks in various areas acceded to this and Tibet fell under Mongolian control. However, Konggar Gyaincain died of disease in Liangzhou. He passed his legacy on to his elder nephew Pagba, the fifth ancestral master of the Sagya Sect and he brought Tibet into the big family of multi-ethnic China.

In 1264, the nobles of Mongolia unified the whole of China. Kublai Khan established the central regime of the Yuan Dynasty in Beijing. All the tribes of Tibet submitted to its authority, ending Tibet's long-term chaotic situation with separatist regimes. Tibet formally became an administrative region under the jurisdiction of the Central Government of China.

Absorbing the local political and religious heads of Tibet to participate in the central regime and strengthening the domination of the Central Government over Tibet was an important policy of the Yuan court in exercising sovereignty over Tibet. In 1270, Kublai Khan conferred the titles "State Tutor" and "Imperial Tutor" on Pagba who accompanied him for nine years. Furthermore, the Zongzhi Yuan or the Council for the General Governance (later renamed as Xuanzheng Yuan or the Council for the Spread of Governance) was established. The Imperial Tutor governed the Buddhist affairs of the empire and the local affairs of Tibet through it. This later became the established practice. The Imperial Tutor also became the senior official of the Central Government directly appointed by the Yuan emperor. According to the uniform official system of the Yuan Dynasty, the highest-ranking official in charge of Tibet was the High Pacification Commissioner, in addition to the head of the Wanhu Office, the head of the 1000-Household Office and pacification commissioner. Many nobles and upper-ranking monks were given official titles. The Yuan Dynasty stipulated that all the ecclesiastic and secular officials were subject to the leadership of the Zongzhi Yuan (Xuanzheng Yuan). The pacification commissioners and heads of the Wanhu Office were nominated by the Yuan Imperial Tutor or the Xuanzheng Yuan and appointed by the emperor. The Central Government also dispatched officials concerned to check the registered permanent households, establish post houses, improve the tax system and at the same time, introduce the calendar and part of the criminal law of Yuan Dynasty to Tibet. Subsequently, the Yuan emperor also conferred the title "Great Precious Dharma King" upon Pagba and the title "Sagya Dharma King" upon Chagna Dorje. At that time, the Sagya area was the center of Tibet in terms of politics, religion, military affairs, economy and culture, and was called the Sagya regime historically.

Tibet formally became an important part of China in the Yuan Dynasty. That was the inevitable trend of the internal historical development of China (including Tibet) and the certain result of the development of the close relationship between Tibetan people and the peoples of other ethnic groups of China formed through long-term political, economic and cultural exchanges as well as the requirement of the common benefit. The heads of the Sagya Sect made active contribution to the historical achievements in resisting foreign invasion and consolidating the southwestern frontier of the homeland.

With the support of the Central Government, the heads of the Sagya Sect gained political and religious domination over Tibet. They called up craftsmen and workers to expand the Northern Sagya Monastery and then build the Southern Sagya Monastery. The northern monastery is in ruins but the southern one remains intact (1957)