Manganese dioxide nanostructures have been synthesized by hydrothermal synthetical method. The crystallographic structure, morphology, and electrochemical properties of obtained MnO2 are examined by XRD, TEM, cyclic voltammetry, and galvanostatic charge–discharge tests. The results showed that the electrochemical properties of MnO2 were strongly affected by the crystallographic structure and morphology. The controlling crystallographic structure of MnO2 can be obtained by altering the molar ratio of KMnO4/MnSO4. The morphology was affected by the hydrothermal dwell time and temperature. The optimal synthetic conditions are as follows: the initial molar ratio of KMnO4/MnSO4 is 3:1, the reaction lasts 2 h at 120 °C, and the filling factor is 90%. In these prepared conditions, the MnO2 with the maximum specific capacitance of 259 F g−1 can be obtained. Prepared δ-MnO2 has a good layer structure and exhibits nanoflower morphology. The XRD studies show that the crystalline degree of this sample is lower, and the average grain size is about 8.3 nm. These results indicate that the product may have potential applications in areas such as electrode materials of supercapacitor and other new storing energy system.