Bosten Lake is an important region of Northwest China that has transformed from a freshwater lake to a saltwater lake since the 1970s. The water quality in the Bosten Lake basin is important for social and economic development, and nitrogen (N) and phosphorus (P) are the key indicators of water quality. The land use data, precipitation data and Digital Elevation Model (DEM) data with the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model were used to simulate the N and P exports of the Bosten Lake basin. The spatial and temporal dynamics of nitrogen and phosphorus exports, and the response of nitrogen and phosphorus exports to land use change and precipitation change were analyzed between 2000 and 2015. The results show that the amount of N and P exports increased during 2000-2015, and the N and P exports are mainly distributed around Bosten Lake. The N and P exports are greatly affected by cultivated land, built-up areas and grassland, while they are less affected by other land use types. The high precipitation areas with small exports of N and P are mainly distributed in mountain areas, while small precipitation areas with large exports of N and P are distributed in plains where the cultivated land and built-up areas are concentrated. The InVEST model can be used in Northwest China, and the statistical downscaling of reanalysis precipitation data can be used in the InVEST model to improve the simulation accuracy in the data scarce regions of Northwest China.