In this study, taking Xiaojiang Watershed of the Three Gorges Reservoir Area as the research object, comprehensively considering the effects of land system, aquatic system, and socio-economic system on the water environment, an index system of integrated water environment regionalization was established, and the basic unit of division was developed under the watershed DEM. In accordance with the method of dominant factors and space overlay, combined with GIS software, integrated water environment regionalization in Xiaojiang Watershed was separated into three zones, i.e. water conservation and ecological conservation zone in the north, pollution control zone in the south, and eutrophication control zone on the mainstream area of Xiaojiang Watershed, respectively. And according to the characteristics and the main environmental problems of the region, put forward environmental protection requirements and measures. In the water conservation and ecological conservation zone, vegetation are not high, and degradation is obvious, requesting to protect existing forest, prohibite excessive deforestation, and facilitate afforestation; in the pollution control zone, forest and grass cover is low, soil erosion is very serious, and industrial pollution emission is the most important factor causing changes in water quality, needing to take pollution control as the main approach; Xiaojiang Watershed is the largest fluctuation band in Three Gorges Reservoir eutrophication control area, requiring proper resettlement, while focusing on strengthening eutrophication management. By exploring the integrated environmental management approach in Xiaojiang Watershed, we proposed zone management of water environment as a new idea, in order to improve the management of water environment in China.