Global climate change is becoming increasingly severe, and soil microorganisms, as the main drivers of terrestrial ecosystem functions and processes, are key drivers of carbon cycling and play an important role in it. Enhancing the carbon sequestration potential of soil through the fixation of CO2 by microorganisms could help achieve the major strategic goal of 'dual carbon'. This article summarized the main ecological functions of soil microorganisms, focusing on the main processes of soil organic carbon input, sequestration, decomposition, and mineralization. It systematically reviewed the important functions of microorganisms in the carbon cycle of ecosystems, as well as the effects of climate conditions, soil physicochemical properties, and human activities on microbially mediated carbon cycling. On this basis, the opportunities and challenges of current soil microbial research were proposed. In the future, it is necessary to strengthen the understanding of regulatory mechanisms of microbially mediated macro genes/macro metabolism, proteomics, and enzymology. Combined with the Global Microbial Program, a carbon cycle model involving microorganisms should be developed to improve the predictive ability of soil as a carbon sink. This approach would help explain the dynamics of terrestrial ecosystem carbon pools and the uncertainty of soil carbon sinks from the perspective of microbial carbon sequestration. It would also provide a theoretical basis for improving terrestrial carbon cycle models under global climate change.