Manganese dioxides (MnO2) with controllable crystalline structure were synthesized by varying the synthesis conditions through a hydrothermal route with KMnO4 and MnSO4·H2O as precursors. Crystalline structures and morphologies of the samples were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy. The paper studied the nanowires growth mechanism under different experimental conditions, and the resulting lithium storage performance of MnO2 nanowires with different crystalline structure was also discussed.