Rechargeable aqueous Zn/α-MnO2 batteries have drawn enormous interest due to low cost, safety, and high energy density as a promising alternative to Li-ion batteries. In contrast, the reaction mechanism of charge storage still remains ambiguous owing to the complexity of side reactions in aqueous electrolytes. This report explored the fundamental reaction mechanism of Zn/α-MnO2 based on first-principles calculation. Zn4SO4(OH)6·xH2O (ZHS) is deposited from the irreversibly dissolved Mn as well as H+ intercalation at a similar voltage range from the first discharge. ZHS is then transformed to ZnMn3O7·3H2O (Zn inserted layered chalcophanite) with distorted α-MnO2 formation at a slightly low voltage range compared with the initial ZHS formation during the charge. Chalcophanite reversibly transformed to ZHS again at the second discharge. In addition, ZHS and chalcophanite are very inactive for ionic and electronic transports due to the high migration barrier of Zn2+ and H+ and large band gap. It is inferred that the reversible transformation from ZHS to chalcophanite and vice versa is the dominant reaction mechanism and can also degrade electrochemical properties by forming distorted α-MnO2 and limiting ion intercalation into the electrode. In addition, the reversible transformation occurs in a similar voltage range (ΔV = 230 mV) with Zn2+ and H+ intercalations. Considering that the surface of α-MnO2 mainly experiences severe side reactions, TiO2 coating, indicating thermodynamical stability in mildly acidic aqueous electrolyte and very low Zn migration barrier, would be a remedy for better performance by conducting Zn and protecting side reactions for aqueous Zn-ion battery cathode. This study provides fundamental insight for developing promising aqueous Zn-ion batteries.