Zn-ion batteries are emerging energy storage systems eligible for large-scale applications, such as electric vehicles. These batteries consist of totally environmentally-benign electrode materials and potentially manufactured very economically. Although Zn/α-MnO2 systems produce high energy densities of 225 Wh kg(-1), larger than those of conventional Mg-ion batteries, they show significant capacity fading during long-term cycling and suffer from poor performance at high current rates. To solve these problems, the concrete reaction mechanism between α-MnO2 and zinc ions that occur on the cathode must be elucidated. Here, we report the intercalation mechanism of zinc ions into α-MnO2 during discharge, which involves a reversible phase transition of MnO2 from tunneled to layered polymorphs by electrochemical reactions. This transition is initiated by the dissolution of manganese from α-MnO2 during discharge process to form layered Zn-birnessite. The original tunneled structure is recovered by the incorporation of manganese ions back into the layers of Zn-birnessite during charge process.