The major basins in Qinghai Province were divided and a SWAT model was built to simulate the change processes of average daily and monthly runoff. The measured values and simulated values of runoff were compared and the model’s simulation results were evaluated, in order to analyze the precision and applicability of the model. The results show that the SWAT model is not applicable to the Qaidam Basin. However, it shows a strong performance and applicability in the basins supplied mainly by precipitation, glaciers, and snowmelt in cold regions and plateau areas.