Rechargeable aqueous zinc–manganese oxides batteries have been considered as a promising battery system due to their intrinsic safety, high theoretical capacity, low cost and environmental friendliness. However, some problems of manganese oxides still restrict the future application of zinc–manganese oxides batteries, such as the structural instability upon cycling, low electrical conductivity and complicated charge-discharge process. Therefore, the modification of Mn-based cathodes, especially the most widely used MnO2, is essential to alleviate these problems and improve the electrochemical performance of zinc–manganese oxides batteries. Herein, this review briefly introduces the evolution of primary Zn–MnO2 batteries to rechargeable zinc–manganese oxides batteries and illustrates the crystal structure characteristics of different MnO2. According to the electrolyte environment with different pH values, the complex energy storage mechanisms of MnO2 are classified and deeply discussed, hoping to provide readers with a clear understanding. Meanwhile, based on the different charge storage processes, the modification strategies of Mn-based cathodes have been systematically and comprehensively summarized from the aspects of structural stability, interface stability and electrical conductivity improvement (ion insertion/extraction process), electrolyte engineering, substrate modification and battery structure design (deposition/dissolution process). Furthermore, the current challenges related to enhancing the stability of Mn-based cathodes, along with some perspectives towards mechanism exploration, material modification and the development of zinc–manganese oxides batteries are also highlighted. Based on the above points, this review will provide guidance and contribute to the future research of zinc–manganese oxides batteries.