Abstract: The Yangtze River Economic Belt, as the largest economic belt in the river basin in the world, is an important new engine for China’s “new normal” economic development. In order to ensure the healthy development of the Yangtze River Economic Belt, China’s government attaches importance to ecological protection, especially the sustainable utilization of water resources. The 11 provinces and cities along the Yangtze River economic belt were regarded as the research object. Based on the concept of “economic-environment-society sustainable green development”, the SE-SBM model and the ML index were established to quantitatively analyze the efficiency of green water resources during the period 2002~2016. Research showed that: (1) the Yangtze River Economic Belt green water resources efficiency showed a slight downward trend and an obvious regional difference, the upstream basin and downstream basin showed decreased, the middle reaches of the river basin was stable and low;(2) the average water resources in Chongqing, Guizhou, Shanghai, Zhejiang reached the effective rate of DEA, the effective value in Jiangxi, Hubei was at a low level and the water resources utilization efficiency fluctuation in Jiangsu, Yunnan was obvious; (3) the index of technological progress was the main factor affecting the efficiency of water resources. The following suggestions were made in this article: build regional systematic development, realize coordinated economic development, improve the technical efficiency， increase the water saving technology, implement the “three water common governance” and strengthen the management of water resources to promote the rational utilization of water resources in the Yangtze River Economic Belt.