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 (EFd) 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.