Abstract: By fully considering the effect of precipitation and terrain on pollutant transport, in order to solve the problems of the quantitative estimation and comprehensive evaluation of agricultural non-point source pollution in regions with sparse data, taking Gulin river basin within the territory of Gulin county as an example, the quantitative estimation for three kinds of pollution sources and four kinds of pollutants in the study area was given by combining improved export coefficient method and source strength coefficient method. The equal standard pollution load method was adopted to evaluate agricultural non-point source pollution in the region. The results showed: the study area of agricultural non-point source pollution was serious; the main pollution sources are rural residents living sewage and livestock breeding, accounting for 74.19% of the total equal standard pollution load; the main pollutants are TN, TP and NH3-N, accounting for 95.83% of the total equal standard pollution load. The towns that had larger pollution contribution were Gulin, Shuangsha and Shibao, accounting for 23.32% of the total equal standard pollution load. According to the results of comprehensive evaluation, it is still necessary to strengthen the organic waste management in the basin, such as rural residents living sewage and livestock breeding waste, reasonably use fertilizers, and reduce the loss of nitrogen and phosphorus.