In order to analyze the effects and existing problems of water diversion in Inner Qinhuai River, a river network was generalized by MIKE11 model, and a onedimension mathematical model of the river network was set up. Taking the typical dry season as an example, NH3N concentration of six control sections were selected as the assessment index of water quality, and a validated model was applied to simulate and calculate the effects of water diversion. The results show that the Inner Qinhuai River is seriously polluted, and the water quality and the flow of water diversion are not up to the requirements of flushing pollutants, and the water quality in water source area should be improved and the flow of water diversion should be increased. There are blind spots of water diversion in every water diversion line, and we should take 4 lines of diverting water jointly to flush pollutants.