There is a coupling and coordination relationship between water use efficiency and industrial structure. Taking 11 provinces in the Yangtze River Economic Belt from 2010 to 2020 as research samples, this paper uses the coupling coordination degree model to measure the coupling coordination relationship between water use efficiency and industrial structure, and uses the geographically and temporally weighted regression (GTWR) model to determine the factors affecting the coupling coordination relationship between the two systems. The results are as follows. From 2010 to 2020, the coupling coordination degree of most provinces in the Yangtze River Economic Belt fluctuated and increased, and formed a spatial agglomeration state of “high in the east and low in the west”, with Shanghai and Chongqing as the “core”. From 2010 to 2020, the center of gravity of the coupling coordination degree of the upstream, middle and downstream shows a trend of migration to the south, north and northwest, and the agglomeration of different watersheds is also different. The influence of various factors on the coupling coordination degree has significant temporal and spatial non-stationarity and heterogeneity. Among them, the dependence on foreign capital, technological innovation, residents' education and water resources possession are the leading influencing factors of the coupling coordination of the Yangtze River Economic Belt.