This paper systematically combs through the historical archives related to Tibet during the Qing Dynasty to examine the Qing Dynasty’s mechanisms of sovereignty over Xizang and their evolution. The study reveals that the Qing Dynasty formed a triangular framework centered on imperial authority, consisting of “central government—provinces—tribal territories”, which effectively achieved long-term and stable governance over Xizang. The tributary authority of Xizang underwent a historical evolution from the Khutans’ court to the Kashag office and the Prince of the Commandery system, and then to the authority of the Amban in Tibet. Each iteration was the result of structural changes in the territorial framework. Through an in-depth analysis of the relationship between imperial authority and the Gelug Sect, this paper demonstrates that Xizang during the Qing Dynasty consistently maintained a political form of separation between religion and state rather than integration: the pure spirit of imperial authority contained no elements of the Gelug Sect’s theocratic nature, and the tributary authority was independent of the Gelug Sect’s religious power. This research clarifies the traditional perception of “Xizang’s integration of religion and state”, reveals the institutional foundation of Xizang’s sovereignty during the Qing Dynasty, and holds significant academic and practical value for understanding the historical relationship between the central government and the Tibetan region.