This research used the improved export coefficient model to estimate non-point source load in sub-watersheds and a self-organizing map model to identify the correlation relationship of factors, that can be affected by non-point source load in Yangtze River Basin. Research results indicate that total nitrogen load is 4.87 - 15.53 kg/ha; total phosphorus load is 0.18 - 0.51 kg/ha; Dong Ting Lake sub-basin has the lowest contribution value of total nitrogen and phosphorus; Tai Lake sub-basin has the highest contribution load of total nitrogen and total phosphorus; Jinsha River sub-basin reveals the highest value of total nitrogen and phosphorus contribution on grassy land and desert land; Tai Lake sub-basin has the highest total nitrogen and total phosphorus load on forest, agricultural land, and urban construction land. The correlation relationship of factors reveals a very close correlation with each other as precipitation, total nitrogen load, and total phosphorus load factors have correlation in the highest value, in which total nitrogen load and total phosphorus load factors have a close correlation with each other from the lowest value to highest value; wetland and barren land factors correlate with the lowest value and the highest value; agricultural land, forestland, and grassy land factors correlate with one another in the high value and the highest value. The forest cover rate factor, as well as the population factor, does not correlate with other factors.