Abstract: The application of biochar in agriculture and the environment has attracted widespread concern. Biochar can enhance soil fertility and reduce toxic effects on soil ecosystems through the fixation and degradation of soil pollutants. The metabolic activity of soil microorganisms is the main driving force in soil element cycles and organic pollutant degradation and is an important index reflecting soil health. However, the understanding of the differences in microbial metabolic activities under the influence of different types of biochar is still incomplete, impeding its sustainable development and application; therefore, it is necessary to investigate the application of biochar to soil microorganisms. This review summarized the mechanisms by which biochar (derived from different raw material sources and pyrolysis temperatures) on soil microbial abundance, diversity, community structure, and activity changes to deeply explore the positive or negative effects of biochar on soil microorganisms. We also focused on the electron transfer process of microbes mediated by biochar, soil fertility improvement induced by biochar-microbe interaction, pollution remediation, and pathogenic microorganism control. The porous structure of biochar provides habitats for microorganisms, while its mineral content can provide nutrients, and high-temperature biochar can increase the pH of acidic soil, providing a suitable environment for the growth of microorganisms. The functional groups with redox activity in biochar can mediate the electron transfer process and promote microbial metabolism. However, the polycyclic aromatic hydrocarbons, volatile organic compounds, environmentally persistent free radicals, and heavy metals contained in biochar have inhibitory effects on the growth and metabolism of microorganisms. Nevertheless, aging and pickling treatments can effectively reduce their toxicity. The effects of biochar and microorganisms on soil fertility improvement, pollution remediation, control of pathogenic microorganisms, and the related mechanisms were also discussed. In practical applications in agriculture, it was found that biochar can promote the abundance and metabolic activity of functional microorganisms such as nitrogen-fixing, phosphorus-dissolving, potassium-dissolving, and pollutant-degrading bacteria. Therefore, under the joint action of biochar and microorganisms, soil fertility can be improved, polluted soil can be repaired, and the detrimental effects of pathogenic microorganisms on crops can be controlled. Suggestions on the efficient utilization of biochar were put forward, and directions for future research biochar and microorganisms were proposed.