The south-to-north water diversion project is an important part of the national water network. In order to further give play to the optimal allocation capacity of water resources of the south-to-north water diversion project, ensure high-quality south water supply, promote the orderly development of follow-up operation and management, and help the construction of the national water network, based on game theory and supply chain theory, this paper discusses the coordination of the water resources supply chain of the south-to-north water transfer from the perspective of economic benefits and water quality improvement. Based on the generalization and relevant assumptions of the water resources supply system of the south-to-north water diversion project, the market demand function, water quality utility function and water quality improvement cost function of the water resources supply chain are established. The multi-objective models of the water resources supply chain under the centralized decision-making, wholesale price contract and revenue sharing water quality improvement cost sharing contract are constructed respectively, and the corresponding coordination strategies are discussed. Finally, the conclusion is verified by numerical analysis. The research shows that there is a conflict between water quality utility and economic benefits; wholesale price contract can not achieve the coordination of the supply chain; and revenue sharing-water quality improvement cost sharing contract can achieve the coordination of water quality benefit objectives and Pareto improvement of economic objectives.