As first effort in literature, this study proposed a mathematical model for microbial hydrogen consumption of underground hydrogen storage in the depleted reservoir, considering phase-change mechanism in growth-decay of bio-film, methanogen reaction, and mass transfer in the multicomponent flow. Effects of the growth-decay mechanisms of methanogens on pore structure, permeability and gas components, were simulated and analyzed in 2D and 3D porous models. The results indicated that: 1) The potential risk of the clogging of the pore space by microbial community was confirmed. 2) The initial volume fraction of microbial saturation (VFm) has a great effect on the growth and decay mechanism of methanogen which adopts the hydrogen as the energy source. 3) The optimized decay coefficient of the biomass could be achieved to decrease the loss of hydrogen and its purity. 4) The reduction rate of porosity and normalized permeability (KN) was believed to be related to decay-growth mechanism of microbials and the pore structure. The model with a lower porosity would lead to a higher saturation of biofilm-water layer (BWL), as well as a higher reduction of the porosity. The required time to reach the maximum BWL was the same, when assuming the growth process of methanogen was homogeneous and isotopic.