Covalent organic frameworks (COFs) are potentially promising electrode materials for electrochemical charge storage applications thanks to their pre-designable reticular chemistry with atomic precision, allowing precise control of pore size, redox-active functional moieties, and stable covalent frameworks. However, studies on the mechanistic and practical aspects of their zinc-ion storage behavior are still limited. In this study, a strategy to enhance the electrochemical performance of COF cathodes in zinc-ion batteries (ZIBs) by introducing the quinone group into 1,4,5,8,9,12-hexaazatriphenylene-based COFs is reported. Electrochemical characterization demonstrates that the introduction of the quinone groups in the COF significantly pushes up the Zn2+ storage capability against H+ and elevates the average (dis-)charge potential in aqueous ZIBs. Computational and experimental analysis further reveals the favorable redox-active sites that host Zn2+/H+ in COF electrodes and the root cause for the enhanced electrochemical performance. This work demonstrates that molecular engineering of the COF structure is an effective approach to achieve practical charge storage performance.