The challenges associated with the ecological security and aquatic environment of the Three Gorges Reservoir Area are of domestic and international concern. This study aimed to examine the spatial variation characteristics of non-point source pollution output effected by changes in land use and the socio-economic background in the Chongqing section of this reservoir area, since the 156 m water level impoundment in 2006. The following four sites of the Three Gorges Reservoir Area were selected on the basis of typical land use variation model and socio-economic background:Fengjie and Zhongxian counties in the hinterland, Jiangjin district located at the end of the reservoir Area, and Shapingba district in the main urban area. The effects of land-use changes and the social-economic development between 2007 and 2013 on spatial variation of non-point source pollutants such as total nitrogen (TN) and total phosphorus (TP) were analyzed. The land-use types were analyzed using remote-sensing images of 2007, 2010, and 2013. The dynamic export coefficient model was used, and the output coefficient of farmland was amended by varying the amount of fertilizer applied. The results show that during the study period (2007-2013), the output of TN increased from 12126.6 t in 2007 to 12692.3 t in 2013, and the output of TP increased from 394.6 t in 2007 to 407.2t in 2013. Non-point source pollution in Jiangjin district continually increased, and the TN and TP output increased by 28.6% and 24.1%, respectively; the increase could be because of the increasing urbanization in this district. The non-point source pollution declined in Shapingba district over the study period, with rapid expansion of the city, and the TN and TP output decreased by 48.8% and 68.9%, respectively. However, non-point source pollution in Fengjiexian and Zhongxian counties showed little variation across the study period, which could be attributable to the maintenance of traditional agricultural practices. Collectively, these results suggest that different land-use types contribute differently to the total amount of non-point source pollutants:for example, farmland has the biggest impact on the TN and TP load, followed by woodland, grassland, construction land, and unused land.