Abstract: During underground hydrogen storage (UHS), indigenous hydrogenotrophic microorganisms may consume hydrogen through metabolic reactions. These reactions can change the composition of the stored gas. Microbial growth can also form biofilms on grain surfaces. The biofilms may occupy pore space, narrow local flow channels, and reduce reservoir flow capacity. To study the coupling among methanogenic hydrogen consumption, biofilm growth, and pore-throat clogging, a two-dimensional pore-scale model was developed for heterogeneous porous media in depleted gas reservoirs. The model coupled microbial reactions, multicomponent gas transport, and seepage flow. It incorporated hydrogenotrophic methanogenesis, in which H₂ and CO₂ are converted to CH₄. It also incorporated microbial growth and decay, evolution of the biofilm-water layer (BWL), convective and diffusive transport of H₂, CO₂, and CH₄, and the additional flow resistance caused by BWL growth. Normalized permeability was used to describe the overall decline in flow capacity caused by pore clogging. Simulations were carried out under representative hydrogen storage conditions of a block in Shengli Oilfield. The effects of inlet CO₂ concentration, initial BWL water saturation, and initial microbial volume fraction were investigated. The results showed that, under the simulated hydrogen storage conditions representative of a block in Shengli Oilfield, the BWL thickness reached the prescribed maximum value of 20 μm after 110 days. At this stage, the biofilm had substantially occupied some narrow pore throats and reduced the cross-sectional area of local flow channels, leading to progressive pore-throat clogging. The normalized permeability consequently decreased to K_N = 0.713. Increasing the CO₂ concentration promoted methanogenic growth and methane production, which accelerated biofilm development and pore-throat clogging. Increasing the initial BWL water saturation from 0.10 to 0.30 shortened the time required to reach the maximum BWL thickness from 179 to 83 days. Increasing the initial microbial volume fraction from 10⁻⁵ to 10⁻² shortened the clogging time from 183 days to 73 days. These results provide pore-scale mechanistic insights into microbial hydrogen consumption, biofilm-induced flow impairment, and subsequent reservoir-scale evaluation of underground hydrogen storage.