Nanostructured flower-like ϵ-MnO2 and α-MnO2 nanowires were prepared by the microwave-assisted hydrothermal method at 110 °C and 140 °C. The ϵ-nanoflowers are about 500 nm in size and are composed of petals about 100 nm in length, while the α-nanowires are 20-30 μm in diameter and about 1 mm in length. The ϵ-MnO2 demonstrates higher initial discharge capacity, while the α-MnO2 shows greater cycling stability in different voltage ranges. Both phases of MnO2 show better cycling performance in ethylene carbonate (EC)/diethyl carbonate electrolyte (DEC) than in EC/dimethyl carbonate (DMC) electrolyte. The ϵ-MnO2 sample delivered a discharge capacity of 116.2 mAh g−1 for up to 100 cycles, indicating that it is a promising cathode material for lithium ion batteries.