The coordinated development of water resources, economy and ecology in the Yangtze River Basin needs to be improved, and the exploration of the coordination between these three factors is conducive to the sustainable development of the Yangtze River Basin. Taking the 10 provinces and cities of the Yangtze River Basin from 2011 to 2020 as the research objects, we firstly established a coupling coordination model of the water-economy-ecology (WEE) system; secondly, the trend surface was used to map the global distribution of coupling coordination degree, and the local characteristics of the development of coupling coordination degree in the Yangtze River Basin were explored; Thirdly, the spatial autocorrelation analysis was used to analyze the global and local correlations of the coupling coordination degree. Finally, a factor detector was adopted to explore the influencing factors of the coupling coordination degree. The results show that the coupling coordination between the water subsystem, economy subsystem and ecology subsystem of the Yangtze River Basin have been increasing year by year, but the increasing trend varied greatly among different subsystems. Moreover, the coupling coordination of the WEE system showed a U-shaped change in the whole area, with a local trend of “midstream < upstream < downstream”. In the meantime, the level of spatial clustering of WEE system coupling and coordination kept increasing and the local spatial correlation has been improving year by year. So, the main influencing factors of WEE system coupling and coordination can be summarized as water development and utilization, water conditions, economic development level, urbanization level, pollution emission and control. In this regard, the Yangtze River Basin can improve the current situation of the corresponding influencing factors in the region based on the distribution of the coupling coordination degree and the contribution rate of the influencing factors in the future, so as to broaden the space for high-quality development of the provinces and cities in the Yangtze River Basin.