In order to study the sources, export characteristics and influencing factors of nitrate-N, the SWAT model was implemented to simulate the runoff and nitrate-N loads in the Meixi River and Daning River basins in the Three Gorges Reservoir Area (TGRA). Then, the hydrological processes and sources of nitrate-N in the basins were analyzed. Based on the random forest model, the effects of different influencing factors (i.e., climate, land use, soil type and topography) on runoff and nitrate-N loads were also quantified. The results showed that:(1) The nitrate-N load varied significantly among different land use types, and the annual load intensity followed the order of orchard (20.41 kg/hm²)>dryland (12.51 kg/hm²)>paddy field (10.31 kg/hm²)>construction land (7.09 kg/hm²)>forestland (0.62 kg/hm²)>grassland (0.46 kg/hm²). Dryland was found to be the main source of nitrate-N export in the Meixi River (80%) and Daning River basins (67%).(2) The base flow coefficient in the Meixi River and Daning River basins was 67% and 62%, respectively, and base flow was the main transport pathway of nitrate-N, contributing 68% and 60% of nitrate-N export in the two basins, respectively. (3) Runoff distribution and nitrate-N export had obvious seasonal variation, the base flow contributed above 70% to both runoff and nitrate-N in these two basins in the dry season, and surface runoff contributed 36% and 42% to nitrate-N export in the two basins in the rainy season, respectively. (4) Rainfall was the main factor affected total runoff, and soil type was the main factor affected surface runoff and base flow. Land use was the main factor affected nitrate-N in different runoff pathways,followed by soil type, and the sum of their relative importance was over 70%. In conclusion, environmental land use conflicts were the root cause of nitrate-N loss, and source control was still a key of non-point source pollution prevention and control in the TGRA. In addition to surface runoff control, it was urgent to incorporate dry land and orchard base flow pathway control strategies.