Hydrogen is a clean alternative to fossil fuels, emitting only water vapor during combustion. In a future hydrogen economy, large-scale storage will be an important component of the supply chain. Due to its low volumetric density, conventional surface storage methods are inadequate. Underground hydrogen storage (UHS) offers a viable solution, enabling the storage of millions of cubic meters. Among potential geological sites, including salt caverns, aquifers, and depleted gas reservoirs, depleted oil reservoirs show promise. Studying hydrogen interactions with residual oil and reservoir minerals is vital for understanding the properties of hydrogen and the reservoir post-injection. In this study, we employed molecular dynamics simulations to gain molecular-level insights into these interactions. We investigated hydrogen dissolution in oil, adsorption at kaolinite/oil interfaces, the role of CO2 as a cushion gas, and the influence of kaolinite’s hydrophobicity on H2 behavior. The main findings include: (1) hydrogen dissolves more in oil than in water, (2) the introduction of CO2 suppresses hydrogen dissolution in oil and reduces the interfacial tension (IFT) between oil and gas, (3) CO2 decreases H2 partitioning near kaolinite surfaces due to its strong affinity for the hydrophilic gibbsite surface of kaolinite, and (4) CO2 is more effective than H2 in reducing IFT between kaolinite and the oil–gas mixture. These findings emphasize the effectiveness of CO2 as a cushion gas and the important role of clay hydrophobicity in UHS, providing insights that are challenging to obtain experimentally.