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 50AhL-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.