The transformation of the discipline construction system in China from "key" to "firstclass" marks the paradigm shift from key discipline construction through the government selection to firstclass discipline construction through the university competition. The evolution of the discipline construction system passes through three stages: the radical, the progressive, and the fractured institutional change. From the perspective of historical institutionalism, the formation and reform of the discipline construction system are influenced by deep structure factors, such as the economic system, the higher education management system and the value orientation of discipline construction. The discipline construction system shows obvious characteristics of path dependence because of traditional institutional inertia and organizational behavior habitus. The fundamental impetus of the reform of the discipline construction system comes from the game of multiple subjects, policy learning mechanism and external demonstration effect. In practice, the key to the reform of the discipline construction system in China is to reshape the relationship between multiple subjects, perfect the discipline dynamic adjustment mechanism, and improve the discipline assessment system, so as to promote the formation of a new governance pattern of firstclass discipline construction.