Abstract: The core of ecological compensation for inter-basin water transfer project is to coordinate the interest relationship of various stakeholders.In order to ensure the reasonableness and implementability of compensation and promote the sustainable performance of project benefits, from the perspective of cooperative game, the middle Route of South-to-North Water Diversion (SNWD) project was taken as an example in this study. A horizontal ecological compensation standard of inter-basin water transfer project was constructed,based on the Shapley value method by sorting out the response relationship of water use and sewage emissions between the water receiving area, water source area and downstream affected area during the operation of the project and sharing the cost and benefit among the subjects . The results showed that: (1) from 2019 to 2021, the annual ecological compensation required to be paid by the water receiving area was 5.526 billion yuan, 5.483 billion yuan and 6.396 billion yuan respectively. The compensation amount required to be paid by Beijing and Tianjin was higher than other cities; (2)Under the joint influence of the optimal allocation of transferred water and the level of economic development, the value of water resources in Beijing, Hebei and Henan provinces tended to increase, while that in Tianjin city tended to decrease;(3)The compensation funds received by the source and downstream areas made up for some of their own water transfer losses.The funds increased with the increasing benefits of water transfer in the receiving area, which helped to further improve the stability of cooperation. Overall, this study revealed the mechanism of optimal allocation of water resources in inter-basin water transfer projects from the perspective of cooperation, and provided a feasible idea for the determination of the balancing mechanism of project benefits and the accounting of compensation standards.