Unstable supply of renewable energy arises with the inevitable seasonal dependency, which contradicts with periodic energy demand. As hydrogen shows high energy density and mobility, yet low solubility and residual saturation, underground hydrogen storage (UHS) becomes a promising solution of scalable energy storage to rebalance demand and supply. Depleted gas reservoirs (DGR) are one of the most appropriate options for UHS because of the integrity of their caprock and storage system. In this study, we developed a numerical model based on TOUGH+RGB simulator (code) to simulate the flow and thermal transport during UHS in reservoirs such as DGR. Given the different transport and thermodynamic properties of hydrogen, different Equation-of-State (EOS) for modeling the phase behavior of hydrogen-included mixtures are calibrated with literature (lab) data, and further are coupled with the simulator. This benefits our numerical experiments to exam various cushion gas pre-injection strategies for pressure maintenance, boundary conditions, and potential hydrogen leakage into caprock. Hence, we can comprehensively assess the seasonal gas recovery factor of hydrogen stored in DGR. The calculated density of hydrogen-methane mixture based on GERG-2008 EOS and Soave-Redlich-Kwong (SRK) EOS is in perfect agreement with experimental data, while that from Peng-Robinson EOS is not quite consistent. Due to the accuracy and efficiency, SRK EOS is employed in our simulator. Hydrogen injection-idle-withdrawal operation is simulated in a synthetic heterogeneous anticline DGR. Due to gravity segregation, we observe that hydrogen displaces pre-existing methane and resides at the top of the storage zone. When the caprock permeability ranges from 10(-5) to 10(-3) mD, only 0.05% of the injected hydrogen at maximum leaks into the caprock. Besides, an open boundary condition connecting with the storage zone helps the pressure maintenance in the storage and lowers the leakage, since with a close boundary condition the leakage rises to 0.35%. Further, about 1% of injected hydrogen is dissolved into the aqueous phase. Those results demonstrate that UHS in DGR has become a feasible choice. Nevertheless, only about 75% amount of hydrogen can be withdrawn if the bottom-hole pressure of producing well is 2MPa below the reservoir pressure. Therefore, cushion gas is necessary for the UHS project to increase hydrogen recovery. This work provides an in-depth investigation of various physics important to UHS, including EOS, hydrogen transport, capillary pressure, mixing, and dissolution. We quantitatively evaluated the hydrogen loss problem, including leakage to caprock, dissolved in water, and mixing with other gas molecules, which is the first-of-its-kind analysis in literature to the authors’ best knowledge. The modeling study is useful for the feasibility analysis of hydrogen storage in the depleted gas reservoir.