Abstract: From the perspective of the system logic of university governance, the university system interacts with the university governance. The system plays a guiding and restrictive role in the construction of the governance system and the governance practice. Also, the governance practice and governance system contribute to the improvement of the system. The university system is formed in the long-term historical process. It is continuously enriched and developed in the governance practice. It is the result of the interaction between the governance subject and the system practice. The system formed in the governance practice includes both formal systems and informal rules and habits etc. Therefore, the system logic is not to construct the system subjectively, but to modernize the governance system and governance capabilities formed in the interaction of system cognition, system composition, system operation and system behavior and system evaluation. The human factor plays a key role in the improvement of the system, the construction of the governance system and the development of governance capabilities. It is necessary to fully focus on and value and play the role of the human factor, especially the governance subject. The key to the system logic of university governance lies in the integration of “university system” and “university governance”, in order to make the university system transform into a governance system through the construction of institutional mechanisms, and to make the institutional advantages transform into governance efficiency. In the governance practice, it is necessary to address all the system inadequacies, strengthen the executive abilities, and improve the system construction, to gradually finalize the system, and promote the realization of the modernization of university governance.