[Objective] The SWAT model was used to simulate and analyze non-point source pollution in the Heihe upper reservoir in order to provide scientific support for the improvement of water quality of the reservoir.[Methods] The non-point source pollution-SWAT model was used to determine and verify the measured rainfall, monthly runoff, sediment and water quality data of the hydrological stations in the basin from 2002 to 2008.[Results] ① The output of non-point source pollution mainly concentrated in the flood season(June-October) and was positively correlated with rainfall. ② The rainfall within the river basin distributed unevenly and it decreased from the south to the north, from mountain to plain. The runoff depth was positively correlated with rainfall, and the spatial distributions of sediment and non-point source loads were opposite to rainfall. ③ The output of non-point source pollution per unit area varied with land use types. The cultivated land had the largest output, followed by the grassland, and woodland had the least. ④ In different simulation scenarios, the pollution load decreased significantly as the cultivated land decreased. In the aspect of non-point pollution control, forest land converted from cultivated land performed better than the cultivated land and woody forest from cultivated land. The conversion of farmland to forest and grassland could effectively reduce the non-point source pollution load in the basin.[Conclusion] The non-point source pollution of Heihe Reservoir occurred mainly in the downstream flood season from June to October. Returning land from farm to forestry, and reducing fertilization, could effectively control non-point source pollution in the region.