Storing hydrogen in geological formations presents promising targets for large-scale storage. However, ensuring long-term safety requires a detailed understanding of the mutual behavior and interactions of fluid species in nano-and meso-pores within the caprock. In this study, we employed molecular modeling, developed based on leveraging bias forces to maintain a constant composition in the fluid external to the pore, to quantitatively investigate the partitioning of an equimolar mixture of H 2 and cushion gas (CO 2 and CH 4 ) within a bulk reservoir into the finite-size clay minerals (illite and montmorillonite). The results demonstrate that in pores smaller than 0.5 nm, neither H 2 nor cushion gas is diffused into the pore spaces. However, H 2 predominantly occupies spaces between 0.5 and 0.6 nm due to its superior rotational movement flexibility compared to the cushion gas. However, the stronger affinity of cushion gases, especially CO 2 , toward the surface and edges of the clay minerals as well as exchangeable cations makes them the dominant species within pores up to a size of 2 nm. Furthermore, the composition of fluid within a pore becomes similar to that of the overall bulk when the pore thickness exceeds 4 nm. The influence of the negative surface charge of clay minerals on the partitioning of fluid species is limited to nanopore sizes and is particularly notable for H 2 /CO 2 , with illite surfaces demonstrating a greater affinity for CO 2 compared to montmorillonite. Nevertheless, this effect diminishes within the meso-pores of clay minerals. Our findings provide valuable molecular insights into the key relationship between caprock characteristics and H 2 /cushion gas partitioning from a caprock integrity perspective in the H 2 geological storage process.