The Yangtze River Economic Belt (YREB) is a highly influential economic belt and an innovative demonstration belt for the protection and restoration of ecological and environmental systems. The dynamic coordination between economic development system (EDs) and water pollution control capability system (WPCCs) is a critical issue to be solved for regional sustainable development. However, this topic has not been adequately addressed in previous studies. To bridge this gap, this paper analyzed the spatiotemporal differentiation and obstacle factors influencing the coupling coordination between EDs and WPCCs in the Chinese Five-Year Plan based on coupling coordination degree model and obstacle degree model. The main results suggest that: (1) the comprehensive level of the comprehensive level of water pollution control capability presents an upward trend with the increase of economic development. A J-shaped relationship existed between the EDs and WPCCs. (2) the regions with rapid economic growth are mainly distributed in the Shanghai, Zhejiang, Jiangsu, Chongqing, and Sichuan. Moreover, water pollution control capability system shows this pattern, eastern regions > western regions> central regions. (3) the coupling coordination level of each region in the YREB has improved from a moderately unbalanced development level to a superiorly balanced development level from 2006 to 2019. (4) per capita gross domestic product, gross product of tertiary industry, total volume of waste water treated, and per daily volume treated of sewage treatment facilities are the major indexes influencing the coordinated development of the EDs and WPCCs. These finding are conductive to formulating reasonable strategies for water environment protection and sustainable development and providing a direction for urban planning.