Enhanced soil health and greenhouse gas mitigation potential are linked to microbial network restructuring under long-term organic farming

• Organic farming enhanced soil health and reduced N 2 O and CH 4 emissions • Microbial network complexity was inversely linked with soil health under organic systems • Keystone microbial taxa regulated GHG emission pathways and soil processes • Organic system achieved 2.5-fold higher net economic returns than conventional farming Understanding how agricultural management reshapes soil microbial organization to regulate ecosystem functions and greenhouse gas (GHG) dynamics is essential for developing climate-resilient farming systems. Here, we investigated how long-term (15 years) organic farming integrating rice–duck co-culture and hairy vetch rotation affects economic profit, soil health, and GHG emissions. This assessment combined 15 N site preference analysis of nitrous oxide (N 2 O), 13 C-labeled and DNA-based stable isotope probing, and microbial co-occurrence network modeling. Compared with the conventional rice–wheat rotation system, the organic farming system achieved a 2.5-fold increase in net economic profit. Long-term organic management enhanced soil health by restructuring cross-domain microbial networks and altering the abundance of keystone taxa. Microbial network complexity was negatively correlated with soil health, indicating that simplified microbial interaction structures may promote soil functioning. Organic farming reduced N 2 O emissions by 65%, which was associated with a lower nitrifier-to-denitrifier gene ratio and increased nos Z gene abundance. Methane emissions decreased by 12%, driven by a fivefold increase in active methanotrophs. Together, these results provide trait-based evidence linking microbial community organization to soil health improvement and GHG mitigation. Our findings advance fundamental understanding of the ecological mechanisms underlying organic management effects on soil biogeochemistry and offer a theoretical basis for designing low-emission, resilient agricultural systems.