Abstract: According to the requirements of National Action Plan for the Prevention and Control of Water Pollution, rational treatments of subbasin, subregion and substage water sources should be established in the critical watersheds to promote their environmental management based on the control units in the 13th National Five-year Plan. We developed a unit dividing method combining the county administrative boundary and watershed management, integrating natural water characteristics and three-level zoning of water resources. In addition, the factors of pollution distribution, socioeconomic factors, and land use were also considered. Based on the method, the major basins of China are divided into 1784 control units, which facilitate the issue of 343 national control units by Ministry of Environmental Protection. As a result, the water quality need is improved in the 13th National Five-year Plan in June 2016. We hope the method can provide scientific rationale and technical support for the accurate and differentiated watershed environmental management based on control unit with clear responsibility for the local government during 2016-2020.