In this study, the Shanxi Reservoir watershed, which is greatly affected by typhoons, is used as the research object, two daily scale SWAT models are established for the dry and wet seasons. Two different typhoon processes in 2007 and 2008 are selected to analyze the pollutant loads during the typhoon period and the reduction of the pollution loads by filter strips. This study focuses on the pollutant load during the typhoon and the reduction effect of management measures, proves seasonal modeling according to regional climate characteristics dramatically improves the accuracy of the model, broadens the perspective of watershed pollution prevention and control. The results show that: the pollutant output of the Shanxi Reservoir watershed is mainly agricultural land, and is positively correlated with precipitation and runoff; loads of organic nitrogen and nitrate nitrogen during typhoon 1 and typhoon 2 accounted for 22.18% and 9.14%, 22.53%, and 18.08% of the whole year, respectively. The pollution loads of typhoon 2 relative to typhoon 1 is relatively small; when the width of the filter strips reaches 3m, the reduction of ammonia nitrogen loads can reach more than 50%, which proves a visible effect on reducing pollutant loads during typhoons.