Abstract: Microbial testing techniques reveal biogeochemical cycling mechanisms in geothermal systems by resolving microbial community structures and their metabolic functions. In recent years, these techniques have emerged as critical tools for sustainable geothermal exploration and utilization. This review summarizes advances in microbial research within the geothermal field from four perspectives—sampling techniques, analytical testing, scientific research, and engineering applications—and discusses key research directions and future trends. At present, there are three major research hotspots in geothermal microbiology: (1) In terms of the regulatory effects of regional and environmental parameters on microbial communities, the structure of geothermal microbial communities is mainly regulated by geological structure, temperature, pH and other factors, showing regional specificity, but the formation mechanism of community structure under the coupling of multiple factors is still unclear. (2) When microorganisms participate in geochemical cycles, they produce mineral precipitation or secrete extracellular compounds through metabolic activities, thereby affecting the clogging and corrosion of geothermal transmission pipelines, with the difficulty lying in how to regulate the metabolism of harmful microorganisms in engineering. (3) On the basis of the dynamic changes in the diversity of geothermal microbial communities, establishing new methods for tracing inter-well connectivity has become a new research hotspot. In the future, efforts should be directed towards establishing microbial atlas databases for various geothermal types and geological settings; elucidating how sulfate-reducing bacteria, iron bacteria, and other relevant microorganisms contribute to the corrosion and clogging of geothermal transmission pipelines; and proposing targeted development solutions. These advances will effectively facilitate geothermal resource exploration and sustainable development and utilization.