Herein, we show the significantly improved solubility of NDI to ~1.5 M in water by incorporating four quaternary ammonium groups, indicated as ANDI. ANDI was stable during the two electron-transfer processes. As-prepared ANDI molecules were repelled due to the cationic ammonium groups in the neutral electrolyte solution. After the first reduction process, the electron paramagnetic resonance (EPR) signal was negligible despite the formation of ANDI radicals. It suggested the formation of radical π–dimer, (ANDI•–)2, where two NDI radical cores were close. The second reduction process produced monomeric ANDI2– due to the repulsion of the anionic NDI cores. Moreover, the NDI core was attracted to the cationic ammonium wings, forming three-dimensional inter-molecular structures. The inter- and intra-molecular interactions of ANDIs during multiple electron transfers were attributed to excellent capacity retention in RFB tests. Aqueous RFBs consisted of 1 M ANDI as the negative electrolyte (negolyte), NH4I as the positive electrolyte (posolyte), and KCl as the supporting electrolyte. The full cell showed an average voltage of 1.08 V and stable cyclability 500 times, which took 45 days. A capacity-fading rate was estimated to be 0.004% per cycle, and a negligible crossover of ANDI was observed. This study demonstrated variable molecular structures and improved chemical stability of organic redox molecules in RFBs.