Metabolic activity of soil microorganisms is intimately connected with soil functioning and thus a sensitive and universal indicator for evaluating soil quality. All the physicochemical and life processes are accompanied by thermal effects, which can be accurately measured and tracked by isothermal microcalorimetry (IMC). The wide application of IMC has fast driven the research of soil microbial thermodynamics. This review briefly introduces the microcalorimetric technology, the wide application of substrate-induced method to reflect the microbial activity in soil, and the main research teams in the world. Then the review focuses on the main application fields of IMC in soil microbiology. Assimilation efficiency of soil organic carbon can be quantified by metabolic thermodynamics of microorganisms. The lower peak time is generally coupled with higher peak power and constant of growth rate, indicating higher microbial activity. Metabolic quotient of heat (heat output per microbial unit), representing metabolic efficiency of soil organic carbon conversion and utilization, is a good indicator to assess soil quality. The xenobiotic pollutants generally inhibit soil microbial activity. The influencing factors and conditional optimization should be considered during detection process of microcalorimetry. The standardization of microbial growing condition and inducing substrate are also discussed. In addition, the potential prospects in near future are described. The combination of IMC and various technologies is expected to play an important role in research on biogeography of soil microbial structure and activity, climate change and soil quality at large spatial scales, and biological toxicity evaluation of exogenous pollutants in soils.