Manganese (Mn), possessing ample reserves on the earth, exhibits various oxidation states and garners significant attentions within the realm of battery technology. Mn-based flow batteries (MFBs) are recognized as viable contenders for energy storage owing to their environmentally sustainable nature, economic feasibility, and enhanced safety features. Nevertheless, the advancement of MFBs is hindered by contentious reaction mechanisms, suboptimal energy density, and inadequate cycling stability. This review offers a comprehensive analysis of various MFBs based on the specific redox couples utilized in the catholyte, including Mn3+/Mn2+, MnO2/Mn2+, and MnO4-/MnO42-. Moreover, recent advancements and concerns encountered by each type of MFBs are subsequently addressed and discussed in detail. Additionally, the current understanding of the mechanisms for different Mn-based pairs and their potentials for energy storage applications are introduced. Finally, challenges for the future development of MFBs, along with suggested improvement strategies are outlined.