Balancing food security with fertilizer-driven climate impacts remains critical in intensive agriculture. While organic–inorganic substitution enhances soil fertility, its effects on nitrous oxide (N₂O) and nitric oxide (NO) emissions remain uncertain. This study evaluated N₂O/NO emissions, crop yields, and agronomic parameters in a subtropical wheat–maize rotation under four fertilization regimes: inorganic-only (NPK), manure-only (OM), and partial substitution with crop residues (CRNPK, 15%) or manure (OMNPK, 30%), all applied at 280 kg N ha⁻¹ yr⁻¹. Emissions aligned with the dual Arrhenius–Michaelis–Menten kinetics and revised “hole-in-the-pipe” model. Annual direct emission factors (EF_d) for N₂O and NO were 1.01% and 0.11%, respectively, with combined emissions (1.12%) exponentially correlated to soil nitrogen surplus (p < 0.01). CRNPK and OMNPK reduced annual N₂O+NO emissions by 15–154% and enhanced NUE by 10–45% compared with OM, though OMNPK emitted 1.7–2.0 times more N₂O/NO than CRNPK. Sole OM underperformed in yield, while partial substitution—particularly with crop residues—optimized productivity while minimizing environmental risks. By integrating emission modeling and agronomic performance, this study establishes CRNPK as a novel strategy for subtropical cereal systems, reconciling high yields with low greenhouse gas emissions.

The magnitudes and source partitioning of soil dinitrogen (N₂) and nitrous oxide (N₂O) emissions are not well documented, yet. To address both issues for black soil subject to a typical cool temperate climate, soil N₂O and N₂ fluxes following the basal application event of an ammonium-based fertilizer (labeled by ¹⁵N) for maize were simultaneously measured in situ by using the ¹⁵N gas flux (¹⁵NFG) method. During the two-month field experiment, the measured N₂ and N₂O fluxes cumulated to 1.61 ± 0.47 and 0.12 ± 0.01 kg N ha⁻¹, respectively, showing N₂O to N₂O plus N₂ ratios ($R_{{\mathrm{N}}_2\mathrm{O}}$) of 0.02–0.31 (0.15 on average). Temperature was identified as a key factor regulating the total soil N₂ fluxes (r² = 0.27, p < 0.01), despite the N₂ fluxes originated from nitrate denitrification related to dissolved organic carbon concentrations (r² = 0.39, p < 0.01). Differently, both temperature and soil moisture jointly accounted for 85% and 74% of the variances in the N₂O fluxes and the $R_{{\mathrm{N}}_2\mathrm{O}}$ values, respectively (p < 0.01). Moreover, the process(es) other than autotrophic nitrification and heterotrophic denitrification could be of substantial importance for the soil N₂O emissions. Our findings emphasized the importance of temperature in regulating N₂ emissions from black soil and the possible site- and/or time specificity of a soil factors-based parametrization of $R_{{\mathrm{N}}_2\mathrm{O}}$. In addition, this study implicates that labeling a nitrogen substrate of nitrification while using the ¹⁵N enrichment of N₂O is necessary to more accurately quantify total soil N₂ fluxes in situ by using the ¹⁵NFG approach even though further confirmation in future studies is still needed.