The charge storage performances of manganese oxide (MnO2) nanostructures highly depend on their crystallographic phase and structure. In this work, MnO2 nanostructures (α-MnO2, β-MnO2 and δ-MnO2) with high crystallinity and different morphology are prepared through a simple, mild and controllable hydrothermal method at 120 °C. [Mn(C8H4O4) (H2O)2]n, a water insoluble metal-organic framework (Mn-MOF), can efficiently react with KMnO4 at different pH, which results in the generation of α-MnO2, β-MnO2 and δ-MnO2. The size of MnO2 nanostructures can be easily adjusted by controlling the ratio of Mn(II)/Mn(VII). The as-prepared MnO2 nanostructures with different structures and sizes are characterized by X-ray diffraction (XRD), field emission scanning electron microscope (FESEM), X-ray photoelectron spectroscopy (XPS), and N2 adsorption/desorption. Among three samples, the layered δ-MnO2 nanostructures with Mn(II)/Mn(VII) = 2.0 show a specific surface area of 240 m2·g−1, specific capacitance of 416 F·g−1 at 0.5 A·g−1, which can be explained as both adsorption/desorption and intercalation/deintercalation process. The energy density of the asymmetric supercapacitor constructed by MnO2 and activated carbon (AC) is 23.2 W·h·kg−1 at a power density of 425 W·kg−1. The controllable synthesis of MnO2 nanostructures with different crystallographic phases based on Mn-MOF may give further insights into supercapacitors.