Abstract: In recent years, the urbanization rate in Jiangxi and Anhui region of the Yangtze River Basin has been increasing, but due to the lag in the construction of urban sewage collection and treatment facilities, a large number of pollutants have been discharged into the urban water bodies, and the urban water eco-environment has been damaged. Taking 19 cities in the region as the study object, the characteristics of regional urban water eco-environment were summarized from the aspects of water environment quality, water resources, water ecology and water security, and the intrinsic factors causing water eco-environmental problems were analyzed by means of literature survey and calculation of pollution load of relevant pollution sources. The results showed that: urban domestic sources were the largest source of pollution in most cities; low water use efficiency had aggravated urban water shortage; the construction of urbanization had made the lake eutrophication risk prominent, and water ecosystem seriously damaged; the development of non-ferrous metal mining and shipping had caused prominent risk of heavy metal and shipping pollution in rivers and lakes. In view of the above problems, comprehensive treatment countermeasures and suggestions for water eco-environment, including urban point source, non-point source pollution prevention, water-saving city construction, eutrophication risk control and non-ferrous metal and shipping terminal pollution control, were proposed.