With an overall consideration of hydrology, water quality and pollution sources, and the pollution source area, which affect the water quality, the Qinhuai River basin has been simplified as a control unit. Based on the establishment of the control unit water environmental model, the most unfavorable hydrological condition has been set up. The model comprehensively considers the effects of boundary water quality and the response relationship between the water quality of a cross-section and the general population. The allowable discharge of each generalization outfall can be calculated by the response relationship, and the COD, NH3-N, and TP water environment capacity of the control unit can be obtained. As shown in the results: in the near future (2017–2019) with 35% sewage interception and 30 m3/s water diversion; in the long term (after 2020) with 82% sewage interception, the water quality can reach the standard. Combined with the measured calculation, the paper also has made a quantitative analysis of the sharing rate of the main tributary and sewage pump station pollutant flux in the control unit and the whole basin within the administrative district.