Abstract Since specifying the structure during operation tends to be challenging for intrinsically proton‐conducting polymers, it becomes increasingly essential to establish a well‐defined migration path in order to predict the proton conductivity. Zwitterion covalent organic frameworks (ziCOFs) provide a platform in crystal frameworks to investigate the proton transfer mechanism, considering their specific charged channel walls, deprotonation surface, and host–guest interactions. Here, a zwitterion nanoconfined proton‐sieves (ziNPS) with “charged casing” channel of charged pathways is proposed to demonstrate theoretically the effectiveness of proton conduction. Density functional theory and molecular dynamic simulation results show that the ziNPS with different anion groups all achieve a shorter hydrogen bond to increase the dense “hydronium‐water” domain, creating a channel of hydrogen bond networks to provide a long‐range pathway for the proton to migrate. As expected, the proton conductivity test by electrochemical impedance spectroscopy demonstrates the aforementioned concept as well. This research presents a fresh view of the ion conduction mechanism originating from localized zwitterionic units, which can apply to the fabrication of COF‐based proton conductors.