Microporous carbon membranes with tunable micropores are attractive materials for CO2 separations. Tailoring the gas transport channels is an effective strategy to achieve high separation performance, while it remains challenging due to the lack of control over sub-nanopores. Herein, we present an in-situ molecular functionalization strategy wherein the confined sub-nanopore properties are designed by enforcing molecules to diffuse over pores and functionalize the pore affinity. By enforcing oxygen-functionalization, a strong CO2 affinity between the carbon matrix and CO2 molecules is generated, which facilitated CO2 transport, thereby enhancing the CO2 permeability by ∼4.7-fold and without sacrificing molecular sieving ability for gas mixtures, like CO2/N2 and CO2/CH4. The functionalization mechanism was confirmed using reactive force field molecular dynamics (ReaxFF-MD) simulations. Furthermore, this strategy, which was directly applied to hollow fiber membrane modules, provides a facile and scalable approach, and expands the currently limited library of penetrative micropore tailoring of microporous membranes.