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Aqueous organic redox flow batteries (AORFBs) are regarded as one of the most promising battery systems for grid-scale and sustainable energy storage, but the longstanding problems, typically, low energy density and inferior cycling stability, must be resolved. Herein, highly water-soluble naphthalene diimide (NDI) derivatives modified with two positively charged and hydrophilic ammonium terminals are synthesized and used as two-electron anolytes for AORFBs. The redox chemistry of NDI molecules is understood by cyclic voltammetry and the corresponding Pourbaix diagram, indicating the two single-electron processes without being protons under neutral pH conditions. Interestingly, the crossover of 4-ammonium-(2,2,6,6-tetramethylpiperidin-1-yl)oxyl (NMe-TEMPO) species occurs, but the hydrogenation reaction of crossed NMe-TEMPO in the anolyte is significantly inhibited, thus alleviating the capacity degradation of AORFBs. As a result, the NDI/NMe-TEMPO AORFBs deliver no distinct capacity decay over 1300 cycles and a stable cycling life over 3500 cycles with 0.00394% capacity fade rate per cycle, which is one of the representative examples among the existing pH-neutral AORFBs. This work clarifies the capacity decay and two single-electron reduction mechanisms and presents a significant advancement for constructing high-voltage and durable pH-neutral AORFBs based on the two-electron naphthalene diimide and nitroxyl radical systems.