To study the effects of land use and agricultural management on non-point source nitrogen pollution in the watershed,Dan River watershed which is an important water source in the middle route of South-to-North Water Diversion project was selected as study area in this research, SWAT model was applied to simulate the nitrate nitrogen and ammonia nitrogen loads in the watershed, and quantify the contribution of land-use change and fertilization and irrigation measures on the nitrogen pollution loads of the river. The results indicated that:(1) The nitrogen pollution changed in different seasons, the most serious nitrogen pollution was from July to September, with the output of nitrate nitrogen and ammonia nitrogen loads of 734.32, 735.36 t, respectively (total accounting for more than 50% of the nitrate nitrogen and ammonia nitrogen load); (2) The nitrate nitrogen and ammonia nitrogen loads had large spatial difference, and the pollution increased from the upstream to the downstream. The sub-watershed with high nitrogen pollution load were mainly distributed in Danfeng and Shangnan counties; (3) The situational analysis indicated that when the farmland with slope greater than 15° and 25° in the basin was converted to forest, the nitrate nitrogen and ammonia nitrogen load in the basin decreased by 59.83% and 45.89%, respectively, and the ammonia load decreased by 48.91% and 35.78%, respectively. Both of fertilizer application and irrigation decreased by 20%, nitrate nitrogen load would decrease by 3.63% and 13.26%, and ammonia nitrogen load would decrease by 0.12% and 15.65%, respectively; (4) Cultivated land is the main source of nitrogen pollution in river basin, reducing the amount of fertilizer,irrigation and vegetation restoration in sloping cropland is the key to control non-point source nitrogen pollution in the watershed.