Safety issues of energy storage devices in daily life are receiving growing attention, together with resources and environmental concerns. Aqueous zinc ion batteries (AZIBs) have emerged as promising alternatives for extensive energy storage due to their ultra-high capacity, safety, and eco-friendliness. Manganese-based compounds are key to the functioning of AZIBs as the cathode materials thanks to their high operating voltage, substantial charge storage capacity, and eco-friendly characteristics. Despite these advantages, the development of high-performance Mn-based cathodes still faces the critical challenges of structural instability, manganese dissolution, and the relatively low conductivity. Primarily, the charge storage mechanism of manganese-based AZIBs is complex and subject to debate. In view of the above, this review focuses on the mostly investigated MnO2-based cathodes and comprehensively outlines the charge storage mechanisms of MnO2-based AZIBs. Current optimization strategies are systematically summarized and discussed. At last, the perspectives on elucidating advancing MnO2 cathodes are provided from the mechanistic, synthetic, and application-oriented aspects.