Abstract: The ecological compensation of inter-basin water transfer project is an effective way to solve the coordinated development of water resources ecological environment protection and economic development between the project water source area and the water receiving area.Based on the evolutionary game theory,this paper constructs an evolutionary game model of ecological compensation for inter-basin water transfer projects,and analyzes the interest demands and compensation behaviors among the local governments in the water source area,the water receiving area,and the higher-level governments. An empirical research is done on the ecological compensation of the eastern route of South-to-North Water Transfer Project. The research shows that it is difficult to achieve the optimal stable equilibrium strategy（water source area protection,water receiving area compensation）in the water source area and water receiving area of the inter-basin water transfer project without the supervision of the higher government. The optimal stable equilibrium strategy is realized and the best social benefits are achieved.In addition,the weighted moving average method is introduced to measure the emission rights of the water source area of the eastern route of South-to-North Water Transfer Project from 2014 to 2019,which clarifies the changes of pollution discharge in the water source area. Based on the emission trading method,the ecological compensation standards of the whole water source area from 2014 to 2019 were determined to be 26,113,398,507,421,and 328 million yuan respectively,and the compensation standards changed with the change of water transfer;The scope of ecological compensation constraints and incentives for the East Route Project to achieve the optimal stable equilibrium strategy,clarifies that the higher the government imposes on the water source area or the water receiving area unilaterally fails to fulfill the obligation,the greater the penalty,the easier it is to achieve the optimal stable equilibrium strategy and restrict the incentive funds not less than twice the ecological and environmental protection investment in the water source area and the ecological compensation fee in the water receiving area are necessary conditions to achieve the optimal stable and balanced strategy,and provide a decision-making basis and thinking methods for the construction of the ecological compensation mechanism for the eastern route of South-to-North Water Transfer Project.