Chemical nitrogen (N) fertilizer has long been used to help meet the increasing food demands in China, the top N fertilizer consumer in the world. Growing concerns have been raised on the impacts of N fertilizer uses on food security and climate change, which is lack of quantification. Here we use a carbon–nitrogen (C–N) coupled ecosystem model, to quantify the food benefit and climate consequence of agronomic N addition in China over the six decades from 1949 to 2008. Results show that N fertilizer-induced crop yield and soil C sequestration had reached their peaks, while nitrous oxide (N2O) emission continued rising as N was added. Since the early 2000s, stimulation of excessive N fertilizer uses to global climate warming through N2O emission was estimated to outweigh their climate benefit in increasing CO2 uptake. The net warming effect of N fertilizer uses, mainly centered in the North China Plain and the middle and lower reaches of Yangtze River Basin, with N2O emission completely counteracting or even exceeding, by more than a factor of 2, the CO2 sink. If we reduced the current N fertilizer level by 60% in ‘over-fertilized’ areas, N2O emission would substantially decrease without significantly influencing crop yield and soil C sequestration.