Covalent organic frameworks (COFs), with their structural tunability, high specific surface area, and excellent chemical stability, have attracted increasing attention in the field of proton conductors in recent years. This review systematically summarizes the research progress of COF-based proton conductors, covering proton transport mechanisms, material design strategies, experimental characterization, theoretical simulation methods, and application prospects. Criteria for distinguishing between the Grotthuss mechanism, which involves proton relaying through a hydrogen-bonding network, and the Vehicle mechanism, which entails diffusion of protonated species, have been clarified based on extensive experimental measurements of activation energies and theoretical simulations of proton transport pathways. In general, an activation energy below approximately 0.4 eV suggests dominance of the Grotthuss mechanism, whereas higher values typically indicate the predominance of the Vehicle mechanism. Proton-conducting materials are commonly categorized into intrinsic and extrinsic systems based on the source of protons. Intrinsic systems construct stable conduction pathways by covalent bonding to anchor sulfonic acid groups, phosphate groups, or nitrogen heterocycles. Extrinsic systems are optimized for proton transport by loading H₃PO₄, ionic liquids, or polymers using confinement effects. In terms of experimental characterization techniques, electrochemical impedance spectroscopy (EIS) was employed to measure macroscopic conductivity and activation energy. Simultaneously, solid-state nuclear magnetic resonance (ssNMR) was utilized to the local chemical environment of protons, X-ray photoelectron spectroscopy (XPS) for analyzing the charge distribution of functional groups, and infrared spectroscopy for monitoring chemical bond vibrations and transformations. Furthermore, the potential applications of quasi-elastic neutron scattering (QENS) and isotope tracing techniques in other materials were also briefly discussed. Theoretical simulation methods encompass density functional theory (DFT), for calculating electrostatic potential and, combined with transition state search methods, proton migration energy barriers, classical molecular dynamics (MD), for calculating radial distribution function (RDF) and coordination number, and ab initio molecular dynamics (AIMD), for dynamic tracking of proton migration pathways. These methods have collectively revealed the microscopic regulatory mechanism of proton transport through pore geometry, functional group arrangement, and synergistic effects of hydrogen bonding. Finally, this review analyzes the application prospects of COF proton conductors in electrochemical energy conversion devices. We propose that integrated efforts in the design, experimental characterization, and theoretical simulation of COFs are essential for achieving performance optimization and advancing towards practical application, thereby enhancing proton conduction efficiency and material stability. Future research should integrate high-resolution characterization and multi-scale simulation to gain a comprehensive understanding of the proton transport mechanisms in COF materials, thus accelerating the application of COF-based conductors in promising hydrogen energy technologies.