Geological hydrogen storage in carbonate reservoirs is a promising method for transitioning to clean energy sources. Gas displacement behavior in porous media is critical for evaluating gas saturation, fluid migration, and storage security. Due to the limited studies in this area, a comprehensive experimental and molecular modeling assessment of various gases (CO 2 , CH 4 , N 2 , and H 2 ) and their flow characteristics during drainage displacement in carbonate reservoirs is presented. Core-flooding experiments are performed on dry and brine-saturated limestone samples to examine the impact of capillary and viscous forces on differential pressure profiles. Molecular dynamics (MD) simulations are employed to study potential interactions in fluid−fluid, fluid− rock, and fluid−fluid−rock systems; results indicate that both viscous and capillary forces directly influence differential pressure profiles. The highest average differential pressure is observed with CO 2 injection, while H 2 exhibits the lowest due to differences in viscous forces. The injection of CO 2 also demonstrated the highest water recovery at 42.77%, followed by CH 4 (34.11%), N 2 (29.02%), and H 2 (23.42%). The calculated capillary number values are low (×10 −8 ), suggesting that all gases quickly entered the pores upon injection and acted as nonwetting phases. When the flow rate is reduced to match the H 2 capillary number, the average differential pressure decreases, and water recovery is similar to that of H 2 at 2 cm 3 /min. This indicates that capillary pressure and gas saturation are not significantly affected by the gas type. MD simulations revealed that the contact angle is zero for all systems, confirming that all gases act as nonwetting phases and that capillary pressure variations are due to differences in interfacial tensions and pore radii. Additionally, H 2 adsorption on pure calcite and brine surfaces was found to be lower compared to CO 2 . Through this study, an enhanced understanding of gas drainage displacement behavior and underground hydrogen storage dynamics in carbonate reservoirs is promoted.