Abstract: SWAT model was applied to Three Gorges Reservoir(TGR) region to study the non-point source pollution and identify the key areas of pollution in this research.After the model was established,observed data of hydrological and water quality from 2002 to 2008 were used for the simulation calibration and validation.The simulation for the indicator E_NS(Nash-Suttclife efficiency) of stream flow,sediment,nutrient were satisfying.Pollution source of TGR was studied later.The result showed that upstream input was dominant with 71.71% average contribution rate,non-point source pollution of TGR watershed came second with the maximal contribution rate 33.03%,and point source of TGR watershed was the lowest which accounted for 4.17% at most.Finally,pollution loads per area of TGR were modified.According to the modification,main areas of non-point source pollution were located in the central of TGR watershed mainly,such as the tributary watershed of Xiaojiang River,Tangxi Rive and Daning River.