Abstract: Based on the Inverse Distance Weighted method (IDW), a precipitation interpolation method (IDW-WVT) based on the coupling water vapor transport with IDW method is established. By using the meteorological data in 2009~2013 of 22 meteorological stations in Three Gorges Reservoir area and its surroundings, the IDW-WVT and IDW methods are adopted to simulate the daily precipitation, and the interpolation effects are evaluated by observed precipitation data of 14 precipitation stations in the typical basin, Pengxi River. In addition, the influence of interpolation precipitation on runoff and non-point source pollution process is analyzed by using the Soil and Water Assessment Tool (SWAT). The results show that the IDW-WVT method outperforms the IDW method in terms of precipitation interpolation precision, with 23.1%，16.9% improvement in daily and monthly simulation respectively, and the performance of runoff and non-point source pollution simulations have also been improved by IDW-WVT method.