In this paper, a highly ordered three-dimensional Co3O4@MnO2 hierarchical porous nanoneedle array on nickel foam is fabricated by a facile, stepwise hydrothermal approach. The morphologies evolution of Co3O4 and Co3O4@MnO2 nanostructures upon reaction times and growth temperature are investigated in detail. Moreover, the as-prepared Co3O4@MnO2 hierarchical structures are investigated as anodes for both supercapacitors and Li-ion batteries. When used for supercapacitors, excellent electrochemical performances such as high specific capacitances of 932.8 F g−1 at a scan rate of 10 mV s−1 and 1693.2 F g−1 at a current density of 1 A g−1 as well as long-term cycling stability and high energy density (66.2 W h kg−1 at a power density of 0.25 kW kg−1), which are better than that of the individual component of Co3O4 nanoneedles and MnO2 nanosheets, are obtained. The Co3O4@MnO2 NAs are also tested as anode material for LIBs for the first time, which presents an improved performance with high reversible capacity of 1060 mA h g−1 at a rate of 120 mA g−1, good cycling stability, and rate capability.