Mild aqueous Zn–MnO2 battery attracts lots of attention in energy storage filed due to its low cost, high safety and environmental friendliness. To achieve high-performance in battery, phase evolution processes of MnO2 during synthesis and electrochemical reactions need to be understood. Herein, the phase evolution during microwave hydrothermal and correlated battery performance of β-MnO2 are studied. The results demonstrate a phase evolution mechanism from an initial mixture of vernadite, nsutite, and pyrolusite (β-MnO2) to a final single β-MnO2 phase, along with enhanced structure stability, increased Mn valence, and decreased BET surface area. It is found that only when microwave hydrothermal time (MHT) ≥ 120 min, β-MnO2 showing both high capacity and excellent cycling performance can be obtained. β-MnO2 prepared under a MHT of 120 min shows a high reversible capacity of 288 mA h g−1 with a median voltage of 1.36 V vs. Zn/Zn2+, and high capacity retentions of 91.8% after 200 cycles at 0.5C and 84.3% after 1000 cycles at 4C, respectively. In addition, the formation of inactive ZnMn2O4 during cycling is observed, which contributes to the capacity fading of β-MnO2 after long-term cycling. This research makes a step forward to the practical application of Zn–MnO2 batteries, and contributes to the large-scale energy storage field.