Abstract: Water resources are the material necessity for human survival and development. The implementation of reasonable water resource ecological compensation mechanism plays an important role in promoting ecological protection and coordinating regional economy as well as the social development. Based on a data of 11 provinces and cities along the Yangtze River Economic Belt from 2004 to 2018, this paper examined the ecological compensation efficiency of water resources in the Yangtze River Economic Belt based on the comprehensive performance, water footprint and gray water footprint of each province or city and analyzed the ecological compensation efficiency and the influencing factors by the sequential DEA-SBM method with dual-objective decision-making model. Results show that the Malmquist-Luenberger index, which reflects the changes of water resource ecological compensation efficiency in 11 provinces and cities in the Yangtze River Economic Belt, shows a “W” pattern with some fluctuations during 2005-2018. The overall pattern indicates that high level of the Malmquist-Luenberger index appears in the eastern region and low level in the central and western regions. Factors, including urban-rural consumption equity and water resource ecological protection, have significant positive impacts on the improvement of water resource ecological compensation efficiency in the Yangtze River Economic Belt. Under the regulation of the green synergy level index, the improvement of productive investment and the equity index of urban-rural distribution can promote the improvement of water resource ecological compensation efficiency. Therefore, to improve the ecological compensation efficiency of water resources, this paper suggests three policy measures, including paying attention to the coordinated urban-rural development, strengthening the ecological civilization construction, and improving capital input structure.