With high scalability and independent control over energy and power, redox flow batteries (RFBs) stand out as an important large-scale energy storage system. However, the widespread application of conventional RFBs is limited by the uncompetitive performance, as well as the high cost and environmental concerns associated with the use of metal-based redox species. In consideration of advantageous features such as potentially low cost, vast molecular diversity, and highly tailorable properties, organic and organometallic molecules emerge as promising alternative electroactive species for building sustainable RFBs. This review presents a systematic molecular engineering scheme for designing these novel redox species. We provide detailed synthetic strategies for modifying the organic and organometallic redox species in terms of solubility, redox potential, and molecular size. Recent advances are then introduced covering the reaction mechanisms, specific functionalization methods, and electrochemical performances of redox species classified by their molecular structures. Finally, we conclude with an analysis of the current challenges and perspectives on future directions in this emerging research field.