The impact of non-point source pollution on the aquatic environment caused by surface runoff splash and scour on surface sediments is becoming increasingly prominent and poses a serious threat to water resource security in the Three Gorges Reservoir area. The sponge city-building scheme based on low Impact development (LID) can effectively reduce nutrients pollutants entering water. However, research about the non-point source load reduction by the sponge city in the representative mountain City still remain unclear. In this study, a representative sponge city Yuelai New Town, from Chongqing China, was selected as the research area to establish the Sponge City Aided Design (SCAD) model. In this study, combined with the actual demand for Yuelai New Town construction, a complete and effective urban watershed water system pollution model was established based on the surface pollutant accumulation process and scour process calculation model. The simulation results were in good agreement with the measured data. After the sponge city optimization scheme (SCO), the suspended solid (SS) reduction ratio in Yuelai New Town is 53.7%, the chemical oxygen demand (COD) reduction ratio is 93.0%, the total nitrogen (TN) reduction ratio is 95.9%, and the total phosphorus (TP) reduction ratio is 95.3%, compared with the traditional development (TD). The results will be helpful for promoting this approach in the Three Gorges Reservoir Area and mountain cities in the future.