The activity of methanogenic Archaea in porous formations is influenced by various pore characteristics, including porosity, surface area, and the gas-liquid interfacial area. This study explores the impact of surface area on methanogenic activity using techniques such as MICP, NMR, SEM, and μCT. The cells of Methanothermococcus thermolithotrophicus, ranging from 1 to 2 μm, indicate that pores smaller than this threshold are not accessible for microbial traversal and colonization. Upon normalization of microbial activities based on pore volume and interfacial area, the findings exhibit strong correlations with specific surface areas of accessible pores in the examined rocks, as determined by MICP, NMR, and SEM. These areas ranged from 0.001 to 0.017 m2/g, 0.003–0.024 m2/g, and 0.012–0.02 m2/g, respectively. The normalized activities increase from 0.19 to 0.44 mM/(h·cm3·cm2) with an increase in the specific surface area, varying by method. Furthermore, an empirical model has been established to quantitatively evaluate hydrogen loss during underground hydrogen storage or the efficiency of bio-methanation, incorporating pore volume, specific surface area, and interfacial area.