Aqueous organic flow batteries (AOFBs) hold great potential for large‐scale energy storage, however, scalable, green, and economical synthetic methods for stable organic redox‐active molecules (ORAMs) are still required for their practical applications. Herein, pyrene‐based ORAMs are obtained via an in situ organic electrolysis strategy in a flow cell. It is revealed that the water attacking pyrenes restructured molecules to produce a variety of isomers and dimers during the electrolysis, which can be modulated by regulating the local electron cloud density and steric hindrance of pyrene precursors. As a result, the molecularly reconfigured pyrene‐based catholytes, even without any further purification, achieved a high electrolyte utilization of ≈96% and volumetric capacity above 50 Ah L−1. Inspiringly, remarkable cell stability with almost no capacity decay for ≈70 days is achieved, benefiting from the robust aromatic structure of the pyrene cores. The insights into the in situ electrosynthesis of pyrene‐based ORAMs provided in the work will provide guidance for designing ultra‐stable ORAMs for AOFB applications.