The region retained a degree of political autonomy under the Sakya lama, who was the de jure head of Tibet and a spiritual leader of the Mongol Empire.

Tibet retained nominal power over religious and political affairs, while the Yuan dynasty managed a structural and administrative[4] rule over the region, reinforced by the rare military intervention.

[5] One of the department's purposes was to select a dpon-chen, usually appointed by the lama and confirmed by the Yuan emperor in Dadu (modern-day Beijing).

[6] The arrangement from the priest and patron relationship was mutually advantageous: the Tibetans retained autonomy and received protection from invasions, while the Mongols of the Yuan dynasty gained further legitimacy for their rulers and embraced profound Buddhist philosophical teachings and moral principles.

[16] Kublai's success in succeeding Möngke as Great Khan meant that after 1260, Phagpa and the House of Sakya would only wield greater influence.

[18][19] With the support of Kublai Khan, Chögyal Phagpa established himself and his sect as the preeminent spiritual leader in Tibet, and in the wider Mongol Empire.

[25] The Sakya hegemony over Tibet continued into the middle of the fourteenth century, although it was challenged by a revolt of the Drikung Kagyu sect with the assistance of Duwa[26] of the Chagatai Khanate in 1285.

The revolt was suppressed in 1290 when the Sakyas and the Yuan army under Temür Buqa [zh; ja], Kublai's grandson, burned Drigung Monastery and killed 10,000 people.

As Yuan declined, in Tibet, Tai Situ Changchub Gyaltsen toppled the Sakya and founded the Phagmodrupa dynasty, the rulers of which belonged to the Kagyu sect.

"[29] Nevertheless, the Phagmodrupa founder avoided directly resisting the Yuan court until its fall in 1368, when his successor Jamyang Shakya Gyaltsen decided to open relations with the Ming dynasty, founded by ethnic Han.