Abstract Proton storage in rechargeable aqueous zinc‐ion batteries (ZIBs) is attracting extensive attention owing to the fast kinetics of H + insertion/extraction. However, it has not been achieved in organic materials‐based ZIBs with a mild electrolyte. Now, aqueous ZIBs based on diquinoxalino [2,3‐ a :2′,3′‐ c ] phenazine (HATN) in a mild electrolyte are developed. Electrochemical and structural analysis confirm for the first time that such Zn–HATN batteries experience a H + uptake/removal behavior with highly reversible structural evolution of HATN. The H + uptake/removal endows the Zn–HATN batteries with enhanced electrochemical performance. Proton insertion chemistry will broaden the horizons of aqueous Zn–organic batteries and open up new opportunities to construct high‐performance ZIBs.