Nitrogen (N) management is the key to achieving food security and environmental sustainability. Here we analyse N flows using a localized N management model for wheat, maize and rice in 1,690 Chinese counties, with a breakdown of multiple reactive N (Nr) loss pathways. Results show that the total N input for producing these three staple crops in China was 22.2 Tg N in 2015, of which 7.4 Tg N was harvested as grain N and 4.0 Tg N was Nr losses in the forms of NH₃ (47%), NO_x (10%), N₂O (3%), and leaching and runoff (40%). By assuming a production level equivalent to that of the top 10% of counties with the highest N use efficiency and yields surpassing the regional average, we reveal the possibility of achieving national staple crop production targets while improving net ecosystem economic benefit in 2050 through a 49% reduction (10.4 Tg N) in synthetic N fertilizer inputs and a 52% decrease (2.9 Tg N) in Nr losses.