This paper utilizes SBM(slack based model) to estimate the green efficiency of water resources in Yangtze river economic zone from 2004 to 2018, which is compared with the traditional economic efficiency and environmental efficiency to study its dynamic changes. Moran's index and spatial Dubin model are employed to analyze its spatial autocorrelation and spatial overflow effect to determine the factors influencing water resources green efficiency, in an attempt to promote green use and optimized allocation of water resources in Yangtze river economic zone. Study shows that the green efficiency of water resources in Yangtze river economic zone is declining windingly, more in upper- and middle-stream. The green efficiency of water resources is also of spatial concentration, obviously constrained by its vicinities in economy, environmental regulations, industrialized level and proportion of the third industry, but spatially overflowed in openness, urbanization, resources and agricultural water use rate. This paper presents suggestions on establishing mutual management of eco-environment, boosting openness, intensifying urbanization, improving infrastructures and increasing capital and technical inputs.