Abstract: The non-point source (NPS) pollution is difficult to manage and control due to its complicated generation and formation. Load estimation and source apportionment are important and necessary for efficient NPS control. The pollution load model based on DEM, sub-basins, land use, soil type got with GIS tool and data from study and experiment was used to study pollution sources and calculate the pollution load of non-point source nitrogen and phosphorus in Jinjiang River watershed. The pollution loads of dissolved nitrogen and phosphorus from land runoff, rural domestic sewage and livestock discharge were calculated based on SLURP model and export coefficients model. And pollution loads of adsorbed nitrogen and phosphorus from soil erosion were calculated with USLE equation. The results showed the pollution load of non-point source nitrogen in Jinjiang River watershed was 12 298.95 t/a, most was dissolved nitrogen which taking up to 94.13%. The pollution sources were mainly interrelated with livestock discharge, agricultural field runoff and rural domestic sewage, which contributor ratios were 31.72%、26.38% and 17.44% respectively. For non-point source phosphorus, its pollution load was 667.04 t/a and took up 56.73% and 43.27% for dissolved and adsorbed phosphorus respectively. Soil erosion, agricultural field runoff and rural domestic sewage were the main sources for phosphorus with contribution ratios of 43.27%、21.10% and 12.25% respectively. Therefore, soil erosion, agricultural field runoff and livestock discharge became the main pollution sources to influence load of non-point nitrogen and phosphorus in Jinjiang River watershed and should be controlled firstly.