Aqueous organic redox flow batteries (AORFBs) are a promising technology for large-scale electricity energy storage to realize efficient utilization of intermittent renewable energy. In particular, organic molecules are a class of metal-free compounds that consist of earth-abundant elements with good synthetic tunability, electrochemical reversibility and reaction rates. However, the short cycle lifetime and low capacity of AORFBs act as stumbling blocks for their practical deployment. To circumvent these issues, here, we report molecular engineered dihydroxyanthraquinone (DHAQ)-based alkaline electrolytes. Via computational studies and operando measurements, we initially demonstrate the presence of a hydrogen bond-mediated degradation mechanism of DHAQ molecules during electrochemical reactions. Afterwards, we apply a molecular engineering strategy based on redox-active polymers to develop capacity-boosting composite electrolytes. Indeed, by coupling a 1,5-DHAQ/poly(anthraquinonyl sulfide)/carbon black anolyte and a [Fe(CN)6]3−/4− alkaline catholyte, we report an AORFB capable of delivering a stable cell discharge capacity of about 573 mAh at 20 mA/cm2 after 1100 h of cycling and an average cell discharge voltage of about 0.89 V at the same current density.