Since the 18th CPC National Congress, the CPC Central Committee with Comrade Xi Jinping as the core has attached great importance to water pollution control in the Yangtze River Economic Belt. The mobility of water determines that watershed governance is a systematic project, any individual action cannot fundamentally solve the water pollution problem, and upstream and downstream collaborative governance must be realized. This paper constructs a collaborative water pollution control system in the Yangtze River Economic Belt, which includes an interest incentive mechanism, a supervision mechanism, and a coordination and cooperation mechanism, and calculates the collaborative degree of water pollution control in the Yangtze River Economic Belt by using the composite system coordination degree model. It is found that the overall synergistic management ability of water pollution in the Yangtze River Economic Belt is weak and the regional coordination mechanism is not perfect and mature, mainly manifested by the large difference in regional interest incentive mechanism, insufficient attention to the overall regulatory mechanism and lack of continuity of coordination and cooperation mechanism. Based on this, suggestions for optimizing the level of coordinated water pollution control in the Yangtze River Economic Zone are proposed, including constructing an incentive mechanism for interests, improving the supervision and management mechanism, and establishing a long-term and sustainable coordination mechanism.