In the background of the protection of Yangtze River, realizing high-efficient development of green ecology should be taken as part of the high-quality development of the Yangtze River Economic Belt. Therefore, focusing on the evaluation and improvement of hydropower energy efficiency in Yangtze River and comprehensively considering social, economic and environmental factors, an input-output index system is established. Based on the hydropower-related panel data of the various provinces along Yangtze River Economic Belt from 2008 to 2017, the DEA method is used to evaluate the hydropower energy efficiency of each region. The results show that the hydropower energy efficiency of Yangtze River Economic Belt is at high level as a whole, and Jiangsu Province and Hubei Province are the “benchmarking” regions. The index efficient score of the urban agglomeration in the middle and upper reaches of Yangtze River is generally high. Different provinces have different energy efficiency improvement directions, that is, Jiangsu Province and Zhejiang Province should reduce the investment in human capital, while Anhui Province and Jiangxi Province should increase the equipment utilization hours of the installed hydropower, and Chongqing Municipality and Guizhou Province firstly should develop local economy with high quality and improve the rate of return of the fixed asset investment. Some suggestions are put forward: development of hydropower with high quality, rigid constraint of water resources, establishment of green hydropower certification system, improvement of investment subsidy system, optimization of the balance between supply and demand, and training of high-level talents.