Hydrogen storage in depleted gas reservoirs stands as a pivotal strategy for mitigating the fluctuations in seasonal energy demand. However, the reservoir's rich microbial community relies on H2 as an electron source for survival, with microbial reactions such as methane generation, sulfate reduction, and acetate production being prevalent. These reactions lead to hydrogen loss, gas release, formation acidification due to organic acid production, and pore plugging by metabolic biofilms. This study begins by establishing a homogeneous depleted gas reservoir, where microbial hydrogen-consuming reactions occur in the formation water, resulting in the formation of microbial biofilms adhering to porous media. Subsequently, Sabatier reaction, homoacetogenesis, and sulfate reduction are integrated, with reaction rates being modulated by variable microbial populations. Underground hydrogen storage simulation is conducted over four cycles, employing a technique of injecting gas at lower depths and extracting gas from higher depths. The findings reveal the formation of microbial aggregation zones near the wellbore, with CH4 and H2S representing the highest proportions at 1.1% and 0.54% of the injected hydrogen volume, respectively. As the storage cycles progress, continuous hydrogen consumption by microbes leads to a maximum hydrogen loss of 6.42%, resulting in a decrease in extracted hydrogen purity. Throughout the process, the effective porosity of the reservoir fluctuates within a range of -0.05% to 0.05%, with no significant pH variation observed.