Abstract: In order to study the diversity characteristic and pollution load of non-point source pollution of nitrogen and phosphorus in the Songhua River, and provide a reference for the water environment management, based on remote sensing (RS) and geographic information system (GIS) technique, using the data of digital elevation model (DEM), county statistics and land use in Songhua River Basin in 2008, the space simulation and load estimation of non-point source pollution in the Songhua River Basin was conducted by export coefficient model (ECM), and the diversity of the non-point source pollution characteristics in the basin was analyzed. The results showed that the non-point source total nitrogen (TN) load was 112.99×104 t and total phosphorus (TP) load was 4.05×104 t in the Songhua River Basin in 2008 respectively. Nenjiang River sub-basin was the maximum load of TN and TP which was 52.80×104 t and 1.79×104 t respectively, accounting for 46.09% and 44.14% of the total TN and TP. The maximum load intensity of TN and TP was the second Songhua River sub-basin which was 2.96 t/(km2·a) and 0.11 t/(km2·a) respectively. From the perspective of non-point sources, 95.92×104 t of TN loads and 3.40×104 t of TP loads were caused by anthropogenic activities, accounting for 83.90% and 83.94% of the total TN and TP respectively. Anthropogenic factor is the key of non-point source TN and TP of the Songhua River, natural causes should not be ignored as well. The results can provide reference for water environment management and overall understanding the non-point source pollution of the Songhua River.