Climate-driven changes in winter snow cover alter soil microclimate and hydrology, affecting soil organic carbon (SOC) dynamics, whereas the mechanisms by which long-term deepened snow influences SOC sequestration across soil profiles remain unclear. Through a 7-year snow manipulation experiment in a temperate grassland, we investigated how increased snow depth (ambient, 50, 70, 90 cm) affects SOC sequestration via microbial-mediated pathways in topsoil and subsoil. Our results showed that long-term increased snow significantly promoted total SOC accumulation by 6% (50 cm), 12% (70 cm), and 15% (90 cm) relative to ambient conditions across soil profile (0–70 cm). Increased snow did not increase topsoil SOC storage despite increased plant biomass, litter decomposition, and root exudates, as elevated microbial respiration offset C inputs and enhanced dissolved organic C (DOC) leaching to subsoil. In contrast, subsoil layer exhibited significant SOC accumulation, driven by improved microbial C-use efficiency (by 11%–18%), enhanced fungal growth with only minor increases in respiratory C losses, and preferential accumulation of fungal necromass from fast-growing Ascomycota taxa. The subsoil also effectively intercepted and processed DOC leached from topsoil, forming a vertical C transport-stabilization continuum. Soil protein abundance (indicative of mineral-associated C) increased significantly in both layers, confirming increased snow progressively promoted SOC stabilization. These findings reveal that topsoil maintains C equilibrium through compensating microbial processes, while subsoil acts as a C sink through fungal-mediated pathways. These contrasting mechanisms highlight the need for depth-resolved, microbial process-based models to predict future C sequestration under altered winter precipitation.