Climate-induced changes in snow cover can greatly impact winter soil microclimate and spring water supply. These effects, in turn, can influence plant and microbial activity and the strength of leaching processes, potentially altering the distribution and storage of soil organic carbon (SOC) across different soil depths. However, few studies have examined how changes in snow cover will affect SOC stocks, and even less is known about the impact of snow cover on SOC dynamics along soil profiles. By selecting 11 snow fences along a 570 km climate gradient in Inner Mongolia, covering arid, temperate, and meadow steppes, we measured plant and microbial biomass, community composition, SOC content, and other soil parameters from topsoil to a depth of 60 cm. We found that deepened snow increased aboveground and belowground plant biomass, as well as microbial biomass. Plant and microbial carbon input were positively correlated with grassland SOC stocks. More importantly, we found that deepened snow altered SOC distribution along vertical soil profiles. The increase in SOC caused by deepened snow was much greater in the subsoil (+74.7%; 40–60 cm) than that in the topsoil (+19.0%; 0–5 cm). Additionally, the controls on SOC content under deepened snow differed between the topsoil and subsoil layers. The increase in microbial and root biomass jointly enhanced topsoil C accumulation, while the increase in leaching processes became critical in promoting subsoil C accumulation. We conclude that under deepened snow, the subsoil had a high capacity to sink C by incorporating C leached from the topsoil, suggesting that the subsoil, originally thought to be climate insensitive, could have a higher response to precipitation changes due to vertical C transport. Our study highlights the importance of considering soil depth when assessing the impacts of snow cover changes on SOC dynamics.