Abstract: Over recent years, the natural balance of the nitrogen (N) cycle has been impacted by population growth and the expansion of agricultural and livestock production, which has created various environmental pressures on ecosystems. As a vital ecological barrier and strategic freshwater reserve in the upper Yangtze River, nitrogen management in the Three Gorges Reservoir Area (TGRA) is crucial for promoting sustainable regional development in agriculture and animal husbandry. Using statistical data from 2000 to 2021, this study employed an N flow model to analyze the spatiotemporal evolution, transfer patterns, and environmental N emissions within the region′s agro-pastoral systems. The results indicate that: (1) The agro-pastoral system had an average annual N input of 2.454×10⁶ tons and an output of 2.126×10⁶ tons, resulting in an average surplus of 3.285×10⁵ tons. The spatial distributions of input, output and surplus were similar, with lower values observed in the reservoir head (Yichang) and tail (Chongqing urban area), and higher values in the central reservoir region (northeastern Chongqing). (2) Chemical fertilizer application and feed input were the primary N sources, while livestock manure was the dominant output pathway. (3) The main driving factors influencing the N budget were: population density (29.60%), population size (26.46%), primary industry output value (19.75%), hog inventory (9.19%), and secondary industry output value (2.63%). (4) The average N use efficiency in the TGRA (27.80%) was significantly lower than national average (31%). Environmental N emissions primarily occurred through ammonia volatilization (27.88%-30.03%), livestock excreta discharge (25.42%-30.96%), denitrification (21.87%-25.34%), and leaching (11.21%-14.53%). While the current environmental emission rate (25.24%) has not yet exceeded the EU standard (30%), future environmental pressures may intensify. Given the existing N surplus, the high proportion of sloping farmland, and significant soil erosion risks in the TGRA, we recommend establishing a three-dimensional integrated prevention and control system to improve regional N utilization efficiency and enhance the quality of aquatic ecosystems.