The modernization of college-level governance system is a core link in deepening the comprehensive reform of higher education and stimulating the vitality of grassroots school-running. Currently, this process is confronted with multiple practical dilemmas, mainly including unclear power and responsibility division within the governance structure, imbalance between academic power and administrative power, rigid resource allocation mechanism, poor channels for democratic participation, and insufficient efficiency of institutional supply and implementation. This paper systematically analyzes the underlying causes of the above dilemmas. On this basis, it explores feasible reform paths from five dimensions: optimizing governance structure, improving decision-making mechanisms, innovating resource allocation modes, strengthening institutional implementation efficiency, and building a collaborative governance culture. The research aims to promote the profound transformation of university secondary colleges from traditional administrative management to modern collaborative governance, and lay a solid micro-institutional foundation for the connotative development of higher education.