Anthropogenic inputs of reactive nitrogen (Nr) provide sufficient food, energy, and industrial products to meet human demands; however, only a fraction of Nr is consumed as food and nonfood goods, and the rest is lost to the environment and negatively affects ecosystems. High-resolution studies of nitrogen flows are invaluable to increase nitrogen use efficiencies and reduce environmental emissions. In this study, a comprehensive substance flow analysis of nitrogen for China in 2014 is presented. Based on the conceptual framework, which highlights the key roles of human drivers, the analysis of the synthetic ammonia supply and demand balance shows that 75% of ammonia is used for agricultural purposes. Moreover, the life cycle analysis of food nitrogen shows that human food consumption accounts for approximately 7% of the total Nr inputs. A quantitative analysis of pollutant emissions shows that industrial and crop production are the main sources of atmospheric emissions, while livestock farming and crop production are the main sources of water emissions. Finally, we investigate four scenarios (efficiency improvement, high recycling rate, nitrogen oxide emission reduction, and a combined scenario) and provide relevant policy recommendations (large farm size, standardized agricultural production model, flue gas denitration, etc.) for improving nitrogen management practices.