The turnover and stabilization of soil organic carbon (SOC) play a crucial role in the terrestrial carbon cycle, contributing approximately 25% to natural climate solutions. Particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) are pivotal in the soil carbon dynamics. Soil microorganisms are the primary drivers of the carbon cycle, by decomposing plant residues to form POC via the “ex vivo modification” and accumulating microbial residual carbon via “in vivo turnover”, which then combines with soil minerals to form MAOC. However, the role of microorganisms in POC and MAOC formation is constrained by multiple factors, including nutrient management practices, soil properties, and climatic conditions, which limit the microbial regulation of carbon sequestration in agricultural soils. This review systematically introduced the framework of POC and MAOC. The contributions of growth anabolism (living and residual microorganisms) and non-growth anabolism (enzymes and extracellular polymers) to POC and MAOC were described. It further elucidated the regulatory mechanisms governing POC and MAOC through microbial community structure and physiological functions, whilst analyzing the influencing factors. On this basis, the review systematically considered the mechanisms and approaches by which microorganisms regulate and increase SOC, providing an important basis for constructing a theory of SOC increase based on physical-chemical-biological synergistic regulation.