Promoting the classification-driven reform of higher education institutions to achieve a transition from stratified to classified development is a critical task for deepening reform and advancing China’s goal of becoming an educational powerhouse. Optimizing the impact of key higher education initiatives on school stratification and addressing their potential negative effects are pressing issues. This study systematically reviews the development history of China’s key higher education initiatives, analyzing their influence on school stratification from dimensions such as resource allocation, concentration of key disciplines, and contributions to enrollment opportunities. The findings reveal that these initiatives have intensified stratification within the higher education system, with institutional structures evolving from a pyramidal hierarchy to a more pronounced stratified model. Key disciplines are increasingly concentrated in a few institutions, and the institutional status conferred by these initiatives often creates a “ceiling effect” for non-selected universities. The stratification is further reinforced by the Matthew Effect in resource flows and evaluation practices that prioritize institutional rank, scale, and rankings over intrinsic quality and contributions. To address these challenges, this study proposes expanding the scope of institutions included in key initiatives, shifting support from discipline-focused to institution-based models, and improving classification evaluation systems centered on institutional types, quality, and societal contributions. These measures aim to alleviate the stratification challenges and promote more balanced development within the higher education system.