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Many firms find it challenging to develop innovations, evidenced by the ever-mounting number of university-industry research alliances. This study examines the strategic choices of actors who participate in collaborative innovation alliances involving partnerships between industry and universities (U-I) based on a stochastic evolutionary game model. White noise was introduced to reflect uncertainty and the stochastic interferences caused by the differences between actors. Using the Itô stochastic differential equation theory, we analyze stability issues of player behaviors in the evolution of a collaborative innovation alliance. The results illustrate that improvements in innovation efficiency can contribute to U-I collaborative innovation alliances. High knowledge complementarity appears to be unbeneficial to the stability of these alliances, and controlling knowledge spillovers may suppress free-rider problems from both sides of the game. Our study contributes to innovation research by providing a decision-making reference for the design of U-I cooperation.