Abstract: The development and utilization of water resources is the premise and foundation of the stable development of river basin, and the construction of a reasonable ecological compensation system is an effective way to solve the conflicts of various stakeholders and to guarantee the ecological security in the process of water resources development. Under the background of the Changjiang Economic Belt of ecological compensation mechanism, based on strong mutual benefit main body theory, the evolutionary game method was used to analyze the ecological development and utilization of water resources between the central government, local government and local businesses interests as well as the evolution process of the dynamic compensation behavior. Taking water resources development of Wanzhou District, Chongqing City, which has a complicated interest game relationship, as a case, we carried out an empirical analysis to study the interactive relations of interest among parties and their influence factors with SD simulation. The results showed that in the game between the central government and the local government, the game would reach a Pareto optimal state faster if the central government increases the ecological compensation funds and policy support. In the game between the local government and local enterprises, if the government collected less resource and environment tax, it would encourage the polluting enterprises to actively control and reduce the emission. The system dynamics was used to verify the consistency between the behavior law and the evolution result of various stakeholders of water resources in Wanzhou District. Then corresponding ecological compensation countermeasures are put forward.