As one of the most important causes of water quality deterioration, NPS (non-point source) pollution has become an urgent environmental and livelihood issue. To date, there have been only a few studies focusing on NPS pollution conforming to the estimation, and the pollution sources are mainly concentrated in nitrogen and phosphorus nutrients. Unlike studies that only consider the intensity of nitrogen and phosphorus loads, the NPS pollution risk for the China’s Fuxian Lake Basin was evaluated in this study by using IECM (Improve Export Coefficient Model) and RUSLE (Revised Universal Soil Loss Equation) models to estimate nitrogen and phosphorus loads and soil loss and by using a multi-factor NPS pollution risk assessment index established on the basis of the data mentioned above. First, the results showed that the load intensity of nitrogen and phosphorus pollution in the Fuxian Lake Basin is low, so agricultural production and life are important sources of pollution. Second, the soil loss degree of erosion in the Fuxian Lake is mild, so topography is one of the most important factors affecting soil erosion. Third, the risk of NPS pollution in the Fuxian Lake Basin is at a medium level and its spatial distribution characteristics are similar to the intensity characteristics of nitrogen and phosphorus loss. Nitrogen, phosphorus, sediment, and mean concentrations are important factors affecting NPS pollution. These factors involve both natural and man-made environments. Therefore, it is necessary to comprehensively consider the factors affecting NPS in order to assess the NPS risk more accurately, as well as to better solve the problem of ecological pollution of water resources and to allow environmental restoration.