Current research on Yangtze River basin water pollution control predominantly examines isolated policies while overlooking policy synergy. In light of this, this paper studies the collaborative governance incentive mechanism for water pollution in the Yangtze River basin, by analyzing the policy interaction between the River Chief System and ecological compensation mechanisms, with the aim of contributing to the advancement of water pollution governance efforts in the region. A tripartite evolutionary game framework was constructed involving the central government, upper-reach municipalities, and lower-reach jurisdictions, this study explores the endogenous mechanisms for promoting basin governance under the background of differentiated collaborative strategies and analyzes stability, determining the stability conditions of the game-theoretic agents in the optimal scenarios of water pollution control in the basin. On this basis, using real data from the Tuohu Yangtze River basin for simulation, analyze the decision-making differences of upper reaches and lower reaches under different ecological compensation amounts, reward and punishment levels, and design potential incentive mechanisms. The findings are as follows: (1) The penalties imposed by central governments on lower-level governments fail to compensate for the regulators' own enforcement expenditures, thereby inducing the adoption of lenient regulatory enforcement. Factors influencing the governance strategy choices of the upper reaches mainly include ecological compensation amounts and reward mechanisms, while those for the lower reaches primarily include externalities and reward mechanisms. When upper-reach municipalities and lower-reach jurisdictions confront high ecological compensation and high-reward scenarios, they engage in multi-stage games and eventually evolve to adopt proactive strategies to control regional water pollution. With the joint efforts of local governments, water pollution in the Yangtze River basin will be significantly improved. (2) Setting different ecological compensation amounts and observing the evolution path and results of local governments, the results show that enhancing the basin-wide ecological compensation framework, standardizing compensation standards and elevating compensation rates for upper-reach municipalities of the Yangtze can effectively promote water pollution control efforts in the basin. However, raising compensation amounts for local governments in the lower reaches does not affect their strategy choices. (3) Setting different reward and punishment mechanisms for lower-level governments and observing the evolution path and outcome changes of lower-level governments, the results show that the reward measures from the central government to local governments can accelerate the progress of water pollution governance in the basin. The magnitude of fiscal and political incentives is positively correlated with the optimization of governance speed. While, equivalent rewards prove ineffective in incentivizing upper-reach municipalities of the Yangtze. Furthermore, the punitive measures imposed by central governments on upper reaches and lower reaches governments have a relatively small effect in practical work, and strict punitive measures hinder the governance enthusiasm of lower-level governments, especially in terms of strategic choices for lower reaches. Generally, promoting water pollution control in different areas of the basin requires different policy incentives.