Aqueous organic flow batteries (AOFBs) are a promising technology for large-scale energy storage. The electrolyte solution is significant in determining the battery’s performance, which has so far remained poorly understood, especially for concentrated electrolyte. In this work, by combining nuclear magnetic resonance (NMR) and molecular dynamic simulations, we explored ion pairing behavior in bipyridinium-based concentrated electrolytes for AOFBs. Through ¹H NMR and ³⁵Cl NMR investigation, the anisotropy of ion pairing behavior between the bipyridinium dications and the chloride counterions was demonstrated. The relationship between bipyridinium-based electrolyte structures and their solubility is illustrated. The volume-specific capacity of bipyridinium-based flow batteries varies and differs nearly threefold for 2.50 M electrolytes with different configurations. This work provides new insights for designing electroactive materials and optimizing the performance of AOFBs.