Globally, ecosystems are becoming damaged or degraded due to stresses associated with anthropogenic activities. To identify the quantitative connection between nitrogen fertilizer-related agricultural production processes and ecosystem health, a dose-response approach based on the ReCiPe 2016 method is developed. Rice production had the highest potential ecosystem health risk (EHR) (560 species.yr) in China, while maize and wheat had EHR values of 413 and 252 species.yr, respectively. Both crop type and planting area have great impacts on EHR. Pollutants posing the highest potential harm to ecosystem health were NH3, N2O, and NO3−. Air pollutants, including NH3 and N2O, did more severe damage to ecosystem health than soil or water pollutants. Scenario analysis suggests that if improved efficiency of nitrogen fertilizer use is employed to replace current practices, total EHR would decline by about 28.7- 41.1%. Improved farming practices could change the relationship between grain productivity and agroecosystem health from trade-offs to co-benefits. Results demonstrated that optimizing chemical fertilizer application in agricultural production processes could significantly contribute to the delivery of some Sustainable Development Goals. It suggests that the impacts of agricultural production on the atmospheric environment require further attention.