In comparison with the developing nano-carbon catalysts, some small organic molecules are also emerging as catalysts with typical features, however, their working mechanism is still unclear. Here, we synthesized a series of viologen-based heterogeneous catalysts with the same molecular skeleton but different substituent groups through anion exchange engineering. These viologen-based molecules were used as a model catalyst to investigate the underlying structure–function relationship for small molecules-based H₂O₂ electrosynthesis. Differing from the commonly reported carbon-based electrocatalysts, viologens can produce H₂O₂ in a synergistic manner, which means that viologens can not only directly catalyze oxygen reduction but also serve as a redox mediator. We found that the ring current and H₂O₂ selectivity of viologens deliver an increasing trend with the increase of the alkyl chain length of alkyl-substituted viologens and further increase when using benzyl as the substituent group. As a result, a benzyl-substituted viologen (BV) delivers the best electrocatalytic performance among the samples, including the highest H₂O₂ selectivity of 96.9% at 0.6 V and the largest ring current density of about 13.6 mA·mmol⁻¹. Furthermore, density functional theory (DFT) calculations disclose that the carbon atoms bonded with positively charged N are the active sites and the small highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) energy gap of BV is beneficial to the synergistic mechanism for H₂O₂ production. This work sheds new insight into the efficient H₂O₂ production in a synergistic manner for small molecules-based electrocatalysts.