In this study, we use molecular dynamics (MD) simulation to study pressure-driven CO 2 and CH 4 flows and their slippage behaviors in β-cristobalite mesopores. The result illustrates that both CO 2 and CH 4 have an apparent adsorption layer on pore surface. However, significant differences in gas slippage are observed: CH 4 flow shows considerable slippage, while it is negligible for CO 2 flow. This disparity is attributed to the collective effect of gas molecular configurations and surface structure. The linear molecular structure of CO 2 allows it to align perpendicular to the surface, even penetrating into the surface. Notably, the perpendicular orientation of CO 2 molecules is energetically favored near the center of the equilateral triangle formed by adjacent oxygen atoms on β-cristobalite surface. Conversely, the symmetric molecular structure of CH 4 , coupled with its larger size, prevents its penetration into pore surfaces. Therefore, despite smooth crystalline surfaces, CO 2 topological accessible plane is much more curved than that of CH 4 . Consequently, CO 2 displays hesitating motions undergoing rotational movements, which significantly hinders its slippage. This study highlights the collective influences of gas molecular characteristics and surface structure on gas slippage, affording important insights into gas sequestration and the development of functional materials for gas separation.