Karst caves are considered sinks for atmospheric CH4 due to their sub-atmospheric CH4 concentrations. Isotopic and molecular analyses suggest that methanotrophic bacteria (MOB) play an important role in consumption of CH4 in caves. Previous research has established that the biogeographic patterns of microorganisms exist widely and is created and maintained by different ecological processes. Considering the great potential of cave MOB in CH4 oxidation, understanding the assembly and working mechanisms will have practical implications for understanding and utilizing cave ecological resources. In this review, we have summarized the information collected thus far on CH4 sources and sinks in caves, MOB phylogeny, and MOB ecophysiology. We applied this knowledge to discuss the factors that may influence the composition and distribution of cave MOB communities in the context of karst geology. Finally, we review the relevant methods and theories and discuss the opportunities and challenges involved in the predictive description of microbial processes of cave CH4 consumption.