Due to the politicisation of universities-within-the-state, the state's governance of higher education in China differentiates itself from other countries. This study examines how the Chinese central government adjusts its governance over universities between 1978 and 2018. Based on an extensive analysis of policy documents and scholarly research, this study proposes an analytic framework, comprising the state's governance logics, governance instruments, and institutional demonstrations. The three strategically selected governance instruments, i.e. laws, policies, and finance, are demonstrated through various aspects integral to China's higher education--the dual-goverance structure, appointment of the principal leadership, access to higher education, university and discipline structures, curriculum and ideology, funding and grants, and tuition fees. Based on an in-depth investigation, the study argues that the underlying governance logics of the state are moving from direct controls to indirect supervision; however, despite the increasing university autonomy and academic freedom in some areas, the state has never abdicated the essential power and authority over higher education institutions. This paper contributes to the theoretical and practical understanding of China's governance of higher education in recent decades.