Abstract: Abstract: After changing from upland farming to paddy field in Jiangchuan irrigation area, the grain production continues to increase, but problem of the non-point source pollution occurs predominantly with total nitrogen and total phosphorus. Both paddy fields and upland fields can experience surface runoff of chemical fertilizers and pesticides, but which land use can cause more surface runoff remains largely unknown. There are many point source pollution researches in water systems in China, and the technology and methods are relatively mature. But for agricultural non-point source pollution, most research is done in the south, and less in the northeast of China. Therefore, it is needed for research on surface nutrient or pesticide runoff when changing from upland farming to paddy fields. With the use of GIS and SWAT model, the spatial database and attribute database of the model for the research area were established. The spatial database included digital elevation map (DEM), land use map and soil map. The attribute database basically included the meteorological, soil property, and agricultural management data. Based on the feature of natural rivers distribution on the edge of the irrigation area, we used "burn- in" algorithm to make the artificial canal system network as the water system, and set up the threshold watershed area to delimit sub basin in the river basin. Next, we used LH-OAT method of SWAT model to analyze parameter sensitivity, and selected the important factors for the model output. We then used the measured data of runoff, total nitrogen and total phosphorus from the years of 2008 to 2009 as the calibration period, and years of 2010 to 2013 as validation period to explore the model applicability in the research area. Finally, the nitrogen and phosphorus pollution load in the study area under different scenarios were simulated. These scenarios were: no change of the existing farmland area, 70%, or 50% of land converted to paddy field. The results showed that: compared with the present situation, under 70% and 50% conversion, runoff water was reduced 20.95 and 41.37 mm, respectively. The total nitrogen load was respectively reduced to 27.84 and 48.16 t per year, and the total phosphorus load was respectively reduced to 1.66 and 2.89 t per year. The results showed that upland farmland after converted to paddy field can cause nutrient pollution from runoff to the surface water. The increasing rate of fertilization and irrigation was another variable that led to the increasing fertilizer loss, and the pollutants in the return water and surface runoff were discharged into Songhua River causing enrichment of nutrients in water. Last, both reducing fertilizer application and use of water saving irrigation can control the total N and total P output to some extent by the scenario simulation. After fertilizer uses were decreased by 50%, the total N and the total P load decreased by 25.23% and 16.32%, respectively. In practice, to ensure the grain production and to control the agricultural non-point source pollution to the water system, change of fertilization methods and use of constructed wetland are needed.