Soil Organic Carbon (SOC) is a crucial component of the carbon pool in terrestrial ecosystems because of its high storage capacity and long residence time. Slight changes in the SOC pool have a remarkable impact on terrestrial carbon flux and global climate change. The mechanisms of composition, transformation, and stability of SOC are primarily controlled by soil microbial properties. Therefore, the research results on the formation, transformation, and stabilization of SOC mediated by microorganisms are reviewed here, with the aim to further understand the function of soil carbon sequestration. SOC consists of plant- and microorganisms-driven carbons. Plant carbon is the major source of SOC. Soil microbial activity is the primary driving force of SOC formation, transformation, and stabilization. Soil microorganisms decompose plant carbon to form easy turnover soil particulate organic carbon through the “ex vivo modification” pathway. Microbial Residual Carbon (MRC) produced by soil microorganisms through the “in vivo turnover” pathway and Mineral-Associated Organic Carbon (MAOC) formed by the interaction with soil clay minerals contribute to stable SOC components, of which the contribution rate of MRC to stable SOC has been reported to be 38.74%. The equilibrium between the “priming and ongoing burial effects” regulates the storage and stability of SOC. On a global scale, the microbial activity mediating SOC changes is subject to annual precipitation and soil environmental factors (SOC, TN and pH). In response to global changes, the mechanism of SOC quantity and quality control by coupling plant litter, microbial activity, and soil matrix should be given more attention. In addition, environmental dependence of microbial carbon use efficiency should be focused to improve our understanding of the carbon sequestration effect of soil microorganisms.