Aqueous magnesium ion-based batteries have attracted significant research interest due to the two-electron transfer process, small cation radius, low reduction potential as well as the inert hydrogen evolution reaction. However, the high surface charge density of divalent Mg2+ ions results in sluggish solid-state diffusion kinetics, which significantly limits the number of host materials suitable for effective Mg2+ ion storage. Here, for the first time, covalent organic frameworks (COFs) are explored as host materials for high-rate aqueous Mg2+ ion batteries. Combining electrochemical and spectral characterization with theoretical simulation, a synergistic charge storage mechanism involving the reaction of nitrogen and oxygen bridged by Mg2+ ions is revealed. Using electrochemical analysis, it is shown that the Mg2+ ion diffusion kinetics are dominated by the surface pseudocapacitive behavior in COFs, which achieves a favorable rate performance and durable cyclic stability. This work offers a new perspective on the storage of Mg2+ ions in COF host materials.