This study applied the Soil and Water Assessment Tool (SWAT) to the Shanxi Reservoir watershed, a drinking water source in Zhejiang Province, China. The important sources of non-point source pollution (NPS) in Shanxi reservoir watershed are agricultural fertilizer application, domestic sewage and livestock breeding, this brings new challenges to water source management. The simulated runoff and water quality parameters total nitrogen (TN) were compared to those of the observed values in the watershed. The Nash-Suttcliffe efficiency (NSE) was 0.94 for monthly runoff during the calibration period 2007-2010, and 0.84 during the validation period 2011-2012. The model can well satisfy the simulation of runoff. For monthly TN of Sancha water quality monitoring station, the NSE is 0.7 in the calibration period of March 2009 to April 2011, and 0.75 in the verification period of May 2011 to December 2012. For the Jiujiang water quality monitoring station, the model index parameters are slightly lower than Sancha, but it is also very good for water quality simulation. The four parameters of total nitrogen, organic nitrogen (ORGN), nitrate-nitrogen (NO3-N) and ammonia nitrogen (NH4-N) were used to analyse the nitrogen pollution of Shanxi Reservoir watershed. The multi-year monthly average results of nitrogen pollutant loadings show significant differences, with large fluctuations every month. ORGN and NH4-N showed a consistent trend, showing a steady growth trend from January to June, peaking in August and continuing to decline in other months, and NO3-N peaked in March. The pollution load of TN in Shanxi reservoir watershed ranged from 142.27 kg/km2 to 725.31 kg/km2, showing a large spatial difference. The pollution load of the tributary basin is weaker than that of the main stream, which generally shows an increasing trend from upstream to downstream. Overall, the pollutant load is consistent with land use and agricultural production and living conditions, showing typical characteristics of non-point source pollution. Through the establishment of regional nitrogen pollution model and the study of pollutant distribution characteristics, this study puts forward some suggestions for controlling the nitrogen pollution load of the Shanxi Reservoir watershed, optimizes the agricultural planting mode, and intercepts the pollution sources that are not directly discharged into the water body.