The inherent porosity of covalent organic frameworks (COFs) establishes 1D conduits capable of facilitating swift proton transport while effectively impeding the passage of other species. This characteristic positions them as a promising avenue for engineering advanced proton exchange membranes in the future. However, the precise manner in which the structural attributes of the COF materials facilitate the proton transportation process remains enigmatic. This study delves into the intricacies of the proton transport mechanism within COFs, using the β-ketoenamine-based COFs TpPa and TpPa-SO 3 H as exemplars. By employing ab initio molecular dynamics and reactive force field molecular dynamics simulations, we elucidate the process. Our findings unveil that confined within the pore channels, protons showcase remarkable conductivity, primarily due to the establishment of a hydrogen bond network involving adsorbed water molecules and the COF surface structure. This interaction leads to conductivity levels as impressive as 10 −1 S/cm. Various factors, including humidity levels, functional group decoration, and stacking arrangements, exert varying degrees of influence on the proton conduction process. Moreover, at the interface between the COF and water, the presence of sulfonic acid functional groups significantly reduces the free energy barrier for proton ingress into the pore channels, thereby contributing to the heightened proton conductivity observed in experimental settings. These unveiled transport mechanisms and influencing factors hold promise for guiding the selection and design of proton exchange membranes with exceptional performance.