After Gushri Khan won control of Tibet, he set up the Gandain Phodrang regime by harnessing the power of the Gelug Sect, becoming the actual ruler through Tibet and exercising rule over Gansu, Qinghai, the Kam areas and U-Tsang.

Gushri Khan had perceived the collapse of the Ming Dynasty, and foresaw that the succeeding Qing Dynasty, which rose in the northeast, had the ability to unify the state, so he took active steps to seek new political support.

In 1644, when the Qing court moved its capital to Beijing, closer connections quickly developed with the force of Tibet. In the following year, Gushri Khan sent his son Dorer Jidalaiba Tuertaigyi to Beijing to present Emperor Shunzhi with a letter expressing his submission to the Qing court. He and the fifth Dalai Lama jointly sent envoys to present their gifts to the Qing court, and their efforts were certainly rewarded. Thereafter, nearly every year saw Khans of the Hoshod Mongols and Tibetan local religious leaders sending envoys to offer tribute to the Qing court, and to be well rewarded in return. In order to further strengthen the relationship with the central government, Gushri Khan wrote to the Qing court: "Please invite to Beijing the Dalai Lama, the eminent master with high virtues and great achievements, and he will bring happiness and prosperity if you let his stay with you and recite Buddhist scriptures for you." At the same time, Gushri Khan tried to persuade the Dalai Lama to accept the invitation of the Qing court. In 1652, the ninth year of Qing Dynasty Emperor Shunzhi, the Dalai Lama and his attendents left Tibet to reach Beijing by the end of the year.

In 1654, Gushri Khan passed away, leaving behind a vacuum lasting four years because of the internal struggles among his sons. In the end, they reached agreement that Dashi Bartuer was in charge of various tribes of Qinghai, and Dayan Khan was responsible for the political and religious affairs of Tibet. But they lacked the capacity and prestige of their father, while the fifth Dalai Lama, by counting on the support of the imperial court, won higher influence and prestige throughout Tibet. In 1658, Degba Soinam Rabdan, who had been appointed by the Gushri Khan, also died. After two year’s negotiation, the Dalai Lama succeeded in appointing his close attendant Zongmeiba Chilie Gyamco as Degba, leading to the power to appoint a new Degba being transferred from the Mongolian Khan to the Dalai Lama.

After the demise of the fifth Dalai Lama, the struggle among the ruling classes of Mongolia and Tibet further deepened. Samgyai Gyamco tried to keep and strengthen his position by counting on political plots and armed force, but this did nothing to settle the internal disputes and struggles. When the Qing court suppressed the rebellion of the Zungar Mongols, Samgyai Gyamco went against the historical trend to suppress them, thus arousing the dissatisfaction of the Qing court.