Abstract: Abstract: Non-point source pollution is the main factor affecting water-soil environment. Based on the SWAT model and GIS technology, spatial and temporal distributions of organic nitrogen (ON) and organic phosphorus (OP) were analyzed in Chahe watershed at the lower Yangtze River. Simulation of non-point source pollution was performed under different irrigation methods. The results showed that SWAT model was applicable for the simulation of non-point source pollution in the study area. Precipitation had strong correlation with runoff, ON and OP, with correlation coefficients 0.897, 0.762 and 0.713, respectively. Runoff during flood season accounted for 56.40% of the annual total, while ON and OP accounted for 64.89% and 59.70%, respectively. Loss of ON had a significant correlation with OP loads. At the spatial scale, high loads areas of ON and OP were mainly concentrated in the central and south of the watershed, and as a whole showed a distribution gradually characteristic to the Chahe main channel aggregation with surface runoff. The distribution of ON and OP loads were not only related to the runoff, but also impacted by the land use obviously. Average ON and OP loads of soybean fields were highest at 56.70 and 8.80kg/hm2, respectively, while the total contribution amount of ON and OP in rice fields accounted for 67.87% and 65.72% of the entire watershed, the main contribution of non-point pollution source, respectively. Through scenario simulations, the implementation of optimizing irrigation on rice fields such as shallow irrigation and deep storage, can effectively control nitrogen and phosphorus losses and improve the soil and water environment of small watersheds. This research provides important reference for scientific farmland management of small watershed.