Aims <p>Excessive nitrogen fertilizer use reduces wheat yield and contributes to several environmental problems. The objective of this study was optimizing nitrogen fertilizer application under water-saving conditions of supplemental irrigation can balance grain yield and alleviate global warming potential value.</p> Methods <p>Supplementary irrigation techniques were applied during the jointing and anthesis stages of winter wheat. The effects of four N application treatments, no N treatment, 0 (N0), 150 (N150), 210 (N210) and 270 (N270) kg ha⁻¹, on greenhouse gas emissions, abundance of nitrification and denitrification genes, and grain yield in winter wheat fields were investigated.</p> Results <p>The results indicated that increasing nitrogen fertilizer application significantly enhanced soil inorganic nitrogen content, nitrogen cycling microbial abundance, and greenhouse gas emissions. Over the two-year period, the global warming potential (GWP) associated with N150 and N210 decreased by 35.45%- 39.16% and 19.60%- 27.12%, respectively, compared to N270. The greenhouse gas emission intensity (GHGI) showed no significant difference between N150 and N210 but was markedly lower than that of N270. Additionally, the nitrogen use efficiency (NUE) for N210 and N270 decreased by 21.72% and 42.65%, respectively, compared to N150. Across both growing seasons, the highest grain yield (GY) and nitrogen agronomic efficiency (NAE) were observed in N210.</p> Conclusions <p>Considering both grain yield (GY) and greenhouse gas (GHG) emissions, nitrogen application under water-saving irrigation in the North China Plain should not exceed 210 kg ha⁻¹ to ensure a balance between agricultural productivity and environmental sustainability.</p> Graphical Abstract <p></p>