On the basis of the agricultural non-point source pollution data survey to Daye and Yangxin, the main pollution loads and main pollution factors is calculated through the relevant formulas. Some conclusions are drawn as follow: The emissions of Nitrogen and phosphorus pollutants from chemical fertilizers poultry and aquaculture are 6043.32t/a, 1044.81 t/a. The emissions in Yangxin (2511.88 t/a, 464.68 t/a) was higher than that in Daye (3531.44 t/a, 580.13 t/a). The Pollutants emissions and pollution load are characterized by Poultry> Chemical fertilizers > Aquaculture in Yangxin. But the features of Daye is aquaculture > poultry> synthetic fertilizer. Thought the comparison of the equivalent load, Nitrogen and phosphorus pollutants from aquaculture are identified as the main pollution factors. The results show that Phosphorus is the main controlling factor from Poultry. The emissions concentration of Nitrogen and phosphorus is above the requirements of Grade III on surface water(TN1.0mg/l, TP0.2mg/l). Appropriate control measures are put forward against main pollution sources and main pollution factors.