Viologen and its derivatives have been widely investigated as the electroactive materials in aqueous flow batteries (AFBs). The high redox potential of viologen poses a challenge to the AFB's energy density when used as the negative electrolyte. A molecular engineering strategy is developed by inserting an electron‐rich π‐bridge unit (viz. thiophene, furan) between the two pyridiniums to lower the redox potential. The resultant 1,1′‐bis[3‐(trimethylamonium)propyl]‐4,4′‐(2,5‐thiophenediyl)bispyridinium tetrachloride ((ATBPy)Cl4) and 1,1′‐bis[3‐(trimethylamonium)propyl]‐4,4′‐(2,5‐furandiyl)bispyridinium tetrachloride ((AFBPy)Cl4) are investigated by a variety of physiochemical methods to track the structure of the molecule and its evolution during the electrochemical reaction. A flow battery is assembled to verify the applicability of (ATBPy)Cl4 with 1‐(1‐oxyl‐2,2,6,6‐tetramethylpiperidin‐4‐yl)‐1′‐(3‐(trimethylammonio)propyl)‐4,4′‐bipyridinium trichloride as the positive electrolyte. Run at the concentration of 1.0 m, the battery achieves a standard cell voltage of 1.51 V, capacity of 23.6 Ah L–1, energy efficiency of 85.7% at 60 mA cm–2, and a record peak power density of 302 mW cm–2, which outperform the reported viologen‐AFBs in literature. This work provides an effective strategy to develop electrochemically active compounds with tunable redox potential and superior chemical stability by molecule engineering.