[Objective] Understanding the diversity of methanogenic communities in the deep environment is the basis for exploring the origin of early life, extreme environmental life and regulating methane production. However, the diversity of methanogenic communities in the deep carbonate karst-fracture geothermal water is still unclear. [Methods] The deep geothermal water samples were collected for methanogenic marker gene mcrA-based high-throughput sequencing by the pumping tests performed in the geothermal scientific drilling holes located in the Jizhong geothermal area, China to explore the diversity of methanogenic communities in the deep carbonate rock karst-fracture geothermal water. [Results] Results showed that 3 classes, 4 orders and 8 genera of methanogenic communities were detected in the deep geothermal water, of which Methanothermobacter, belonging to Euryarchaeota, Methanobacteria and Methanobacteriales, was dominant methanogens, accounting for 99.85% of the total sequences. The dominant species based on mcrA was closely affiliated with Methanothermobacter wolfeii (similarity 99%, accounting for 71%). The metabolic pathway of methanogens was mainly the pathway of CO2 reduction. The compositions of methanogenic communities in different samples were different, but Methanothermobacter was a dominant genus in all of the samples, accounting for more than 99.77%. [Conclusions] This study reveals that the deep geothermal water from the carbonate rock karst-fracture geothermal reservoirs contains relatively abundant but extremely uneven compositions of methanogenic communities and expands the habitat type of Methanothermobacter, which provides scientific basis for further studying the function of methanogens in the earth ecosystem.