This study examined the effects of governance in higher education on the changing structures of universities, focusing on three major aspects: the marketization of higher education, new circuits of academic capitalist knowledge, and the quality of higher education. To do so, the study employed time-series-cross-sectional (TSCS) data analysis with random effects models. The primary focus was to conduct empirical research utilizing comparative indicators and analytical tools for cross-national analysis, and to complement existing qualitative studies on the changing nature of universities. The results suggest the following: First, reductions in public subsidies for higher education may encourage higher education institutions to enter into market activities. Second, the results provide evidence that new circuits of knowledge, namely, academic capitalist knowledge regimes, are more highly associated with market activities such as university-industry collaboration and R&D performance compared to public good knowledge regime. Third, the results suggest that quality of higher education institutions is positively correlated with both public subsidies in higher education and university-industry collaboration.