To prevent and control the non-point source pollution in the Nishan Reservoir Basin, an established and calibrated SWAT model was utilized to simulate the results of best management practices (BMPs), and to analyze the temporal and spatial variation characteristics of total nitrogen (TN) and total phosphorus (TP) reduction. The results showed that the practices of 50% reduction of fertilizer use, ecological ditch, vegetation buffer zone and returning farmland to forest had a significant effect on the reduction of TN and TP, which reduced the TN and TP by 48.22% and 52.41%, 36.86% and 52.73%, 38.31% and 51.00%, 45.17% and 38.53%, respectively. The maximum reduction of TN and TP by BMPs was in wet period (June to September); however, different BMPs had great effects on the spatial distribution of TN and TP reduction. According to the current situation in the basin, the combined practices of 50% reduction of fertilizer use, ecological ditch and vegetation buffer zone should be applied to high-risk pollution areas with abundant farmlands, large rainfall and steep slopes; whereas the combined low cost practices of reduction of fertilizer use and contour cultivation should be arranged for low-risk pollution areas. Moreover, returning farmland to forest should be actively carried out.