From the 1st Dalai Lama Gendun Zhuba to the 4th Dalai Lama Yundain Gyaco, all of them were religious figures, neither had mastered the power of Tibet, nor had much influence. During that period, Pagzhu Kagyu Authority ruled Tibet, which lasted for 264 years (1354 - 1618 A.D.).
After the Parinirvana of the 4th Dalai Lama, it was time when the Pagzhu regime was toppled by Tsangpa Khan from the Karma Kagyu Sect who hated the Gelug Sect. In order to change the situation of Karma regime's persecution of the Gelug Sect, and to avoid the lineage extermination, the 4th Panchen Lama plotted to seek help from the Gushri Khan, the leader who occupied Qinghai Province at that time, and they finally decided to pledge allegiance to the Qing Dynasty. After a series of wars, Tsangpa Khan was captured in 1642, signifyinig the end of the Karma regime.
Gushri Khan invited the 5th Dalai Lama to the Samdruptse and "handed over" the political authority and his clans to the 5th Dalai Lama in order to show his piety to Buddhism. Therefore, the 5th Dalai Lama set up the Gandain Phodrang Regime in the name of the Gandain Phodrang Palace of the Drepung Monastery.
The 5th Dalai Lama sent Sechi Qugye (in ancient books also noted as Yilagu Kesan) as a delegate for the Qing Dynasty, who arrived in Shenyang (now capital city of Liaoning Province) in 1642, which was warmly welcomed by emperor of the Qing emperor Huang Taiji (1592-1643) even wrote a letter to award the 5th Dalai Lama.
Emperor Shun Zhi (1638-1661) sent envoys to condole the Dalai Lama and the Panchen Lama and offered alms to show his support after he broke through entered Shanhaiguan Pass, signifying that the Ming Dynasty was overthrown by the Qing Dynasty
In 1652, the 5th Dalai Lama led more than 3,000 followers to pay respect to Emperor Shun Zhi and was awarded a golden seal and golden imperial edict with the title of "a kind Buddhist lama in the west region benefiting the entire world".
Since then, the central government of the Qing Dynasty officially affirmed the Dalai Lama's position as the religious leader in Tibetan and Mongolian areas.
In 1751, the Qing Dynasty accredited the 7th Dalai Lama to head Gaxag (the local government of Tibet) and allowed them to inherit the power, which was strengthened step by step with the support of the central government of the Qing Dynasty.