Lithology plays a crucial role in controlling the soil carbon (C) pool in forest ecosystems. The dynamics of soil organic C (SOC) are significantly influenced by the composition and function of the soil microbial community. However, the mechanisms by which lithology influences SOC and the involvement of microbes in this process remain unclear. To assess both the accrual and stability of SOC, we analyzed its content and physical composition by fractionating it into labile particulate organic C (POC) and stable mineral-associated organic C (MAOC). The study was conducted in two representative plantation coniferous forests developed on karst (limestone) and non-karst (shale) soils, with the aim of elucidating potential microbial regulatory mechanisms underlying lithology-mediated differences in SOC dynamics. Our findings revealed that SOC concentration was significantly higher in karst soils compared to non-karst soils at both depths, primarily due to the greater accumulation of MAOC, while lithology had a different effect on POC between topsoil and subsoil. Interestingly, the ratio of MAOC to POC was higher in karst soils compared to non-karst forests only in subsoils. These results imply the crucial role of lithology on SOC accrual and stability in coniferous forests. Soil nutrients stoichiometry, pH and exchangeable calcium ions (Ca2+) have exerted influence over microbial community composition, whereas microbial biodiversity and life history strategies only affected by soil nutrients. Additionally, structural equation modeling analyses revealed that lithology exerts a stronger influence on SOC than tree species, as lithology affects soil nutrient availability, thereby indirectly regulating the microbial impact on SOC accumulation. Nonetheless, both tree species and lithology significantly influence Ca2+, which indirectly promote SOC accumulation by enhancing the stability of SOC pool. Collectively, our study highlights the key role of lithology in SOC stability and accrual, providing a lithology-dependent linkage between microbial communities and the soil C pool.