It is of great theoretical and practical significance to achieve high-quality development that promotes the transformation of digestion, absorption, and re-innovation to an independent innovation model, actively participating in the restructuring of the industrial chain, and enhancing the status of the Yangtze River Delta in the global innovation chain. This study constructs a tripartite evolutionary game model of collaborative innovation led by the government, participated by upstream enterprises and downstream enterprises. Moreover, this article analyzes the strategic choices of the tripartite entities in the process of collaborative innovation, and the simulation analyzes the influencing factors of the government, upstream enterprises, and downstream enterprises’ collaborative innovation strategy selection. The results indicate that the government, upstream enterprises, and downstream enterprises have different degrees of influence on each other’s willingness to participate. In addition, the analysis proves that government policy support and financial support have different impacts on upstream enterprises and downstream enterprises.