Imine-carbonyl compounds show high-capacity due to Zn2+/H+ co-storage, however, the impact of C═N and C═O interactions on Zn2+/H+ coordination remains underexplored. To address this, small organic molecules with the same number of active sites but differing positions of C═O and C═N groups are designed and selected. It is found that different relative positions cause spatial restriction of the C═N active site, making the bonding mode of zinc ions shift from N─Zn─O to O─Zn─O. Moreover, O─Zn─O exhibits a larger bond order and higher stability compared to N─Zn─O. The larger bond order enhanced the stability of the reduction products, resulting in better battery cycling performance. In addition, the co-storage of Zn2+/H+ reduces the Gibbs free energy change of the reaction, increases the discharge voltage, and results in a flatter discharge plateau. This study serves as an important guide for designing high-performance organic cathode materials.