Aqueous zinc ion batteries (AZIBs) are a promising energy storage technology due to their cost-effectiveness and safety. Organic materials with sustainable and designable structures are of great interest as AZIBs cathodes. However, small molecules in organic cathode materials face dissolution problems and suboptimal cycle life, whereas large molecules suffer from a low theoretical capacity due to their inert carbon skeletons. Here, we designed two covalent organic framework (COF) materials (benzoquinoxaline benzoquinone-based COF (BB-COF) and triquinoxalinylene benzoquinone-based COF (TB-COF)) with the same structure and number of energy storage groups to investigate the correlation between the densities of active sites and electrochemical performance. We conclude that the electrochemical behavior of organic conjugate-based energy storage materials lacks a linear correlation with active site quantity. Adjusting active site densities is crucial for material advancement. BB-COF and TB-COF with dual active sites (C=O and C=N) exhibit distinct characteristics. TB-COF, which has dense active groups, shows a high initial capacity (222 mAh g⁻¹). Conversely, BB-COF, which features a large conjugated ring diameter, presents superior rate performance and enduring cycle stability. It even maintains stable cycling for 2000 cycles at −40 ℃. In-situ electrochemical quartz crystal microbalance tests reveal the energy storage mechanism of BB-COF, in which H⁺ storage is followed by Zn²⁺ storage.