The simulation of nitrogen (N) and phosphorus (P) pollution load structure in Bali Lake basin was performed by SWAT model using the spatial and attribute database acquired through social survey and statistical data. The model was applied and validated based on the data of meteorology, runoff and water quality from 2010 to 2014. The spatial-temporal distribution of N and P in the basin was also studied. The results showed that the urban life was the most important source of N and P load, following by agriculture and livestock breeding pollution source, and the least was industry pollution source. The annual TN and TP loads were mainly concentrated in flood season (from May to September) which took up nearly 55% of the whole year load. As the amount of precipitation increased, TN and TP loads increased during flood period, which was mainly due to the increasing of non-point rural living water and agricultural fertilization pollution source with scouring action of the heavy rainfall during flood season. The spatial distribution of N and P was centered on the Jiujiang county, Xunyang and Lushan district as the urban agglomeration area affected by urban sewage pollution.