The construction of hydropower stations will change the original hydrological situation and water environment of the natural river channels, it is necessary to study the backwater effect on the downstream section of the hydropower station caused by its operation and the impact on the water quality of the river. Taking the proposed Xunyang Hydropower Station in Hanjiang River as the study object, we analyzed its impact on the water intake of Mapoling. ECOLab water quality model, which is coupled with two-dimensional hydrodynamic model, was used to simulate and calculate six working conditions. The distribution of flow field and the concentration distribution of chemical oxygen demand (COD), dissolved oxygen (DO) and ammonia nitrogen (NH3—N) at the water intake before and after the construction of the reservoir were compared, and the risk assessment of water quality after the construction of the reservoir was conducted. The results showed that the flow velocity of the water intake reduced to different extents. Compared with the natural river channel, the water quality index of the water intake after the construction of the reservoir only fluctuated slightly and was within the range of the surface water environmental quality class II standard. Under risk conditions, the values of water quality indicators of the water intake were far beyond the limit of surface water environmental quality class II standard, and the safety of water intake could not be guaranteed. It is suggested that Ankang Dam in the upstream of Hanjiang River should discharge water timely. This proposal can provide a theoretical basis for the protection measures of the water intake in the reservoir area of the proposed hydropower station.