Photocatalytic hydrogen peroxide (H2O2) production using covalent organic frameworks (COFs) relies on the concerted operation of two half-reactions: oxygen reduction (ORR) and water oxidation (WOR). A critical limitation arises from the frequent proton and O2 supply-demand imbalance between these processes, which constrains overall H2O2 yields. To address this challenge, a bisite sulfonate-functionalized COF (2-SO3H-COF) is developed that serves as an efficient proton mediator, promoting both solution-phase proton/O2 uptake and rapid intraframework proton transport through hopping mechanisms. The optimized material demonstrates remarkable performance, yielding 4744 µmol g−1 h−1 H2O2 under acidic conditions (pH = 1) and even achieving 11 470 µmol g−1 h−1 in 10% benzyl alcohol solution, which represents a 3.36-fold enhancement over unmodified COFs in deionized water. Isotopic labeling and computational studies elucidate how -SO3H groups facilitate proton conduction from water into the framework while enhancing O2 adsorption, thereby promoting a direct 2e− ORR pathway. When implemented in a flow reactor system, 2-SO3H-COF enables continuous H2O2 production while simultaneously degrading >95% of organic dyes and maintaining 99% antibacterial efficacy. These findings establish a general design principle for proton-regulating photocatalysts and expand the potential of COF materials for sustainable chemistry and environmental applications.