Currently, research on water pollution control in the Yangtze River Basin mostly revolves around a single policy, often neglecting the synergistic effects of strategies. In view of this, this article studies the incentive mechanism for collaborative governance of the upper and lower reaches of the Yangtze River, based on the consideration of specific political power and responsibility sharing, political incentive mechanisms, and horizontal ecological compensation policy coordination. By establishing a tripartite evolutionary game model between the central government, local governments in the upper reaches of the Yangtze River, and local governments in the lower reaches of the Yangtze River, this study explores the design of endogenous mechanisms and potential incentive mechanisms for tripartite collaborative promotion of watershed governance under the background of differentiated collaborative strategies. Real data from the Wujiang Yangtze River, Hanjiang Yangtze River, and Tuohu Yangtze River basins are used for simulation and emulation. Research has found that the central government"s authority and intervention in local watershed governance are relatively limited, leading to the problem of ineffective watershed governance not being further resolved; The formulation of water pollution control strategies by lower level governments depends on the extent to which their financial constraints can be filled by horizontal ecological compensation. Therefore, in specific scenarios, watershed water pollution control has not achieved the expected results. The simulation results of strategy selection indicate that local governments in the upper reaches of the Yangtze River are always more inclined to choose "transfer governance", and the willingness and motivation of officials in the upper reaches of local governments for watershed governance are not strong. Further political arrangements are urgently needed to avoid such behavior.