With the increasing control strength of industrial point source pollution and instant development of agriculture, the proportion of non-point source pollution (NSP) loading occoupied total pollution loading in the Fenghe river watershed is rapidly rising. The SWAT model is applied to simulate the producing and transporting process of runoff, sediment and nitrogen non-point source pollution. The monthly obsereal runoff, sediment and pollutant data from 2001to 2006at the Qindu town hydrological station in the main stream of the Fenghe river were used to calibrate and verify the model. The results of verification show that the model has good adaptability in the watershed and is available. The NSP loading output analysis on spatial and temporal distribution show that the NSP loading output distributes in flood reason and the critical source areas of NSP loading output are the towns as Wuxing, Luanzhen and Ziwu of the Chang′an County in the middle of the watershed, and the towns as Caotang and Qinduzhen in Huxian County in the west of the watershed. The effect simulation of NSP control measures show that the measures such as soil and water conservation, improving application methods of chemical fertilizer, and reasonably reducing fertilizer volume can effectively decrease NSP loading in the watershed.