Since 2013, the Ministry of Water Resources has selected 105 cities as pilot projects for the water ecological civilization city construction. The water ecological civilization city construction has achieved primary results and the first 46 pilot cities had completed the projects by the end of 2017. In order to make full use of the construction experience of the pilot projects, this paper introduces the management method of benchmarking to the water ecological civilization city construction for the first time. Based on the Guideline SL/Z7382016 for the Evaluation of Water Ecological Civilization City Construction, the benchmarking management index system is studied and the benchmarking target selection principles of the water ecological civilization city construction are determined. Then the water ecological civilization city construction of the A city in the middle  downstream of the Yangtze River is taken as an example to illustrate the method and steps of benchmarking management, including index allocation and weight calculation. The gap between A city and the target city is quantified, the seriousness of the existing problems are analyzed, and the key points of attention in the next step of the water ecological civilization city construction are pointed out. The research shows that the benchmarking method can be used to improve the pertinence and effectiveness of the water ecological civilization city construction.