In order to accurately reveal the spatial heterogeneity of non-point source pollution in the Pengxi River Basin of the Three Gorges Reservoir area, this paper establishes a simulation and prediction model for non-point source pollution in the Pengxi River Basin based on the WRF model, which reflects the precipitation on a fine grid with the size of 3 km×3 km. The results show that the simulation accuracy of runoff based on WRF precipitation data is 27% higher than that obtained based on the precipitation data of six meteorological stations in the Pengxi River Basin from 2009 to 2012, and the simulation accuracies of the concentration of total phosphorus(TP)and total nitrogen(TN)are increased by 31% and 36%, respectively. The annual runoff simulated with WRF precipitation data ranges from 3. 528 billion to 5. 404 billion m³, and the average TP and TN loads are 1 151. 35 t/a and 11 759. 72 t/a, respectively. Monitoring data show that the sub-basin units with higher TP and TN non-point source loads in the Pengxi River Basin are concentrated near the river system, with obvious spatial heterogeneity.