The non-point source (NPS) pollution has become an important limitation to the sustainable development of the Three Gorges Reservoir Area (TGRA) water resources. NPS load estimation research has theoretical and realistic significance for water environment security and water pollution control. Therefore, the TGRA was chosen to be the study area, and the export coefficients of different land-use type were calculated through literature consultation method combined with improved observation experiment. The load of total nitrogen (TN) and total phosphorus (TP) of NPS from different pollution sources including farmland, decentralized livestock and poultry breeding and domestic pollution sources were estimated. The results are shown as follows: the order of TN load of different sources in the TGRA from high to low was land use, livestock and poultry breeding, rural life; the TN from land use was 372% higher than that of rural; the order of TP load of different sources in the TGRA from high to low was livestock and poultry breeding, rural life, land use; the TP from livestock and poultry breeding was 114.5% higher than that of land use. Therefore, control of livestock and poultry sewage discharges was the key practice to limit the TP loss, while the optimization of agricultural management was the key practice to control the loss of TN.