Abstract: Hydrogen is prone to leaking through the cap rock in depleted gas reservoirs, making it crucial to understand the sealing characteristics of capillary throats in ensuring the safe storage of hydrogen underground. This study integrates molecular dynamics simulations and pore network modeling to construct kaolinite slit models with varying pore sizes, alongside a pore network model of the cap rock. We simulated the adsorption and diffusion behaviors of four typical gases: hydrogen, methane, ethane, and carbon dioxide, and analyzed how the presence of alkanes and carbon dioxide within the capillary pores affects hydrogen diffusion. Furthermore, we coupled molecular simulation results with the pore network model to assess the diffusion processes of hydrogen, alkanes, and carbon dioxide through the capillary throats of the cap rock, with a particular focus on the diffusion behavior of hydrogen in the presence of methane and carbon dioxide. The results indicate that:①Hydrogen exhibits a lower adsorption energy on the surfaces of kaolinite, resulting in its diffusion coefficient being 1-2 orders of magnitude higher than that of methane, ethane, and carbon dioxide, demonstrating superior permeability. ②The occupancy of adsorption sites on the pore surface by methane and carbon dioxide has both physical and chemical inhibitory effects on the free diffusion of hydrogen. ③The structure of the capillary throat significantly influences the sealing capability of the cap rock, with the connectivity and heterogeneity of pore throat distribution being critical determinants of its sealing performance. ④Although the thickness of the cap rock affects macroscopic permeability, the diffusion process of hydrogen through the cap rock exhibits nonlinear dynamic characteristics, indicating that the diffusion rate decreases over time. This research provides valuable theoretical guidance for risk assessment and site selection in hydrogen storage within depleted gas reservoirs.