Developing climate-smart fertilization strategies is crucial for sustainable agriculture that mitigates greenhouse gas (GHG) emissions without reducing productivity. Although the impacts of integrated organic-inorganic fertilization on GHG emissions are increasingly studied, the relationships between emissions and key soil properties have not been comprehensively quantified in subtropical wheat-maize systems, particularly in long-term field experiments. Using a 21-year wheat-maize rotation system in the Sichuan Basin, China, we evaluated how the integration of different organic-inorganic fertilization strategies affects GHG emissions, key soil properties, and yields. Five treatments were tested: unfertilized control (CK), synthetic fertilizers (NPK), partial substitution of synthetic N with pig slurry (OMNPK) or crop residues (RSDNPK), and biochar addition to synthetic fertilizers (BCNPK). Integrated fertilization strategies enhanced total N (+98 %), soil organic carbon (SOC; +131 %), and microbial biomass C (+185 %) and N (+145 %) compared to CK (P < 0.05). Relative to NPK, OMNPK increased N2O emissions by 82-248 % and exhibited the highest net global warming potential (net GWP; P < 0.05). Conversely, RSDNPK matched NPK's net GWP by offsetting emissions through enhanced SOC sequestration (+110 %) despite elevated seasonal CO2 emissions (29-83 %; P < 0.05). Notably, BCNPK became a net C sink by achieving negative net GWP (-1532.5 kg CO(2)eq ha(-1)). Additionally, multivariate analysis identified dissolved organic C and microbial biomass dynamics as key drivers of N2O and CO2 emissions variations across treatments, explaining treatment-level emission differences. These findings demonstrate that long-term integration of either crop residues or biochar with synthetic fertilizers are climate-smart strategies, providing a sustainable pathway to reconcile agricultural productivity with environmental sustainability in subtropical wheat-maize agroecosystems.