As a necessary supplement to clean renewable energy, aqueous flow batteries have become one of the most promising next-generation energy storage and conversion devices because of their excellent safety, high efficiency, flexibility, low cost, and particular capability of being scaled severally in light of energy and power density. The water-soluble redox-active electrolytes are the core components of aqueous flow batteries. The redox-active organic molecules have leaped to the more important electrolytes than conventional inorganic species because of their structural diversity, tailorability, and potential low cost. Much research work was conducted on organic electrolytes for designing high-performance aqueous flow batteries. The motivation of this review is to summarize and present the structure features, property evaluation methods, performance improvement schemes and battery design principles. The detailed functionalization methods to improve the physical and chemical performances of organic electrolytes including redox potential, reaction kinetic rate, solubility, and permeability have been emphatically provided and analyzed. Meanwhile, the further development prospect of aqueous organic electrolytes was put forward.