<p>Aqueous organic batteries attract attention owing to their intrinsic safety, low cost, and low polarization. However, while most studies focus on molecular design, the influence of supramolecular assembly and crystal structure beyond the molecular scale remains somehow largely overlooked. In this work, a single crystal electrode of aqueous proton batteries, 2,3-Dichloro-1,4-naphthoquinone is investigated by the means of combined characterization techniques including nuclear magnetic resonance, single crystal X ray diffraction, operando X ray diffraction, and cryogenic transmission electron microscopy combined with theoretical calculations. The roles of molecular structure, supramolecular assembly and crystal structure in proton storage performance are elucidated. Notably, the π-donor-acceptor stacked bimolecular pairs form a reinforced 100 facet with the lowest proton adsorption energy, enabling 96.82% capacity utilization. The full cell using this material as negative electrode and lead dioxide as positive electrode delivers stable cycling performance at 5 A g⁻¹ over a wide-temperature from −20 ^oC to 40 ^oC with a capacity retention of 95% after 300 cycles. This work provides insights into the structure property relationships in aqueous organic battery materials across molecular, supramolecular and crystalline levels.</p>