The river basin coordination mechanism is the product of the mature development of modern river basin legislation. There is still a big gap between the coordinated governance of the Yangtze River basin and the overall goal of systematic protection. The coordination mechanism is difficult to meet the needs of long-term management of the river basin, and the collaborative legislation mechanism still needs to be improved, and the lack of cooperation between environmental justice and administrative law enforcement has been restricting the overall coordinated development of the Yangtze River basin. To promote the improvement of the river basin coordination system, it is first necessary to complete the systematic construction of the river basin coordination mechanism, and to clarify the legal positioning and constituent elements of the river basin coordination mechanism. Second, it is necessary to establish an entity agency for basin coordination and clarify its responsibilities and authorities. Third, it is necessary to clarify the operation process of watershed coordination and administrative cooperation. The fourth is to establish detailed rules for the coordination of legislation and cooperation in the basin. Finally, it is necessary to strengthen the overall linkage of the implementation of the river basin coordination law.