Abstract:In order to meet the needs of the control-unit-based water pollution prevention problem in China, we proposed a comprehensive control unit zoning method with the combined basic administrative region and objective watershed management. The method can effectively connect the natural characteristics of watershed water sources, three-level zoning of water resources, and comprehensively consider the pollution distribution, socio-economics and many other factors. The zoning process includes four steps: (1) Generate the multi-level hydrological unit; (2) Identify the multi-element water catchment units; (3) Obtain the control unit with the administrative boundary as the boundary; (4) Check and adjust the results to meet the actual needs. Based on this method, the Yangtze River Basin was divided into 568 control units with a total area of 1.91 million km 2 . These control units were used as the basic unit to analyze the water quality status and the results show that the upper reaches have good water quality, while the lower reaches have poor water quality and more serious water pollution. Our study helps the Ministry of Environmental Protection of China develop the list of control units that are needed to improve water quality during the "13th Five-Year Plan", with a goal to provide technical support for control-unit-based water pollution prevention and control in the future.