Agroforestry systems enhance soil structural stability and optimize carbon-nitrogen coupling through the vertical hierarchical configuration and spatiotemporal complementarity of trees, shrubs, grasses, and crops. This increases their potential for greenhouse gas (GHG) mitigation and carbon sequestration. However, the mechanistic attribution and cross–scale upscaling of GHG fluxes remain constrained by heterogeneity in soil aggregate structure and microhabitats. As a key driver of GHG emissions, soil aggregate stability governs substrate availability, microbial activity, and gas diffusion by shaping pore networks and oxygen-water distribution patterns, which in turn regulate CO2 mineralization, CH4 production and oxidation, and N2O generation via nitrification and denitrification pathways. From the perspectives of hierarchical aggregate theory and micro–ecological process modeling, this review systematically synthesizes the biotic (roots, arbuscular mycorrhizal fungi, microbial mucilage/exudates), physicochemical (organo–mineral associations; iron and aluminum oxides and hydroxides), and management (intercropping, biochar, tillage) drivers of aggregate stability in agroforestry systems, as well as the key pathways and scenario–dependent differences (climate, soil type, and management) through which they affect GHG emissions. Future research directions in this field should focus on elucidating the regulatory effects of root-microbe-aggregate interactions on GHG metabolism; establishing cross-scale research frameworks that integrate in-situ observations with mechanistic models; validating site-specific carbon sequestration and emission reduction technologies through long-term experiments; and predicting the impacts of extreme events and future climate scenarios on system emissions.