In view of the interprovincial water resources management dilemma caused by water supply and demand structure alienation in the Yangtze River Economic Belt, this paper, based on water footprint algorithm related with temporal and spatial variability, takes the water footprint of agriculture, industry, life and ecology as the core issue and carries out the Yangtze River Economic Belt accurate water footprint accounting work. Built on the indexes of water footprint intensity, water footprint land density, it analyzes the law of water footprint structure in the Yangtze River Economic Belt and clarifies the alienation characteristics of water footprint structure between provinces. Research shows that agriculture is the main source of inter provincial water footprint in the Yangtze River; The momentum effect and scale effect are the characteristics of interprovincial water footprint; Ecological endowment and development pattern are the nature of interprovincial water footprint. The key to the coordination development of water resources in the Yangtze River Economic Zone lies in the coordination of three major water footprint leading elements, namely, industrial layout, geographical location and population size.