Multi-major collaborative innovation has a significant supporting effect on the sustainable development of the regional economy. Based on the evolutionary game method, this paper constructs a tripartite game model of government-core enterprises (academic and research) institutions, explores the evolutionary relationship and equilibrium stabilization strategy of the triple game, and clarifies the key factors affecting the strategy selection of each game subject through Matlab simulation. The results of the study show that: (1) The R&D benefit-sharing ratio of industry-university-research collaborative green innovation shows an inverted U-shaped relationship with the behavioral evolution path of industry-university-research, and the inflection point of the inverted U-shaped relationship is the optimal benefit-sharing ratio; (2) Government regulation has a vital role in guiding and correcting the strategic choices of different game subjects, especially the sensitivity of core enterprises to changes in collaborative innovation behavior is much higher than that of academic and research institutions; (3) Moderate government subsidies and greater-than-threshold penalties are conducive to system stability, and the simultaneous action of rewards and punishments is more effective than a single mechanism in stabilizing green innovation ecosystems.