Abstract: The cross-basin water diversion of the Middle Route of the South-to-North Water Diversion Project (SNWDP) is an extremely complex system that involves multiple stakeholders. It is difficult to balance the conflicts in water quantity and water quality among the water source area, the middle and lower reaches area, and the water receiving area involved in the Project. In order to ensure the sustainable exertion of the project’s benefits and the long-term development of the economy and society, a tripartite evolutionary game model was established in this study. Under the constraint and incentive mechanism of the central government, the evolutionary equilibrium strategies of the water source area, the middle and lower reaches area, and the water receiving area were analyzed. The opportunity cost of losses in the water source area, the water resource value of the middle and lower reaches area, and the ecological compensation amounts from the water receiving area to the water source area were calculated, based on the opportunity cost method, the water resource value model, and the cost-sharing model. The sensitivities of cost and fine parameters were analyzed. The results showed that: (1) If a stable strategic equilibrium of the water source area was to be achieved, the fine imposed by the central government on the water source area should be greater than 18.147 billion yuan. If the unit water resource value of the middle and lower reaches area was greater than the unit cost of purchasing water rights, the evolutionary stable strategy could be achieved. The horizontal ecological compensations from the water-receiving area to the water source area and the middle and lower reaches area were 6.091 billion yuan and 1.08 billion yuan, respectively. If a stable strategic equilibrium of the water receiving area was to be achieved, the fine imposed by the central government on the water receiving area should be greater than 7.171 billion yuan. (2) The punishment measures of the central government had a positive incentive effect on the water source area and the water receiving area, and the water receiving area was more sensitive to fines than the water source area. The game system became more difficult to reach an equilibrium state for the higher relevant cost parameters of the water source area and the middle and lower reaches area.