Considerable efforts have been devoted to pursue both higher energy density and power density for a number of energy storage devices. Here we report a hierarchical CoxFe3−xO4 nanoarray which is directly grown on three-dimensional conductive substrates by a facile two-step hydrothermal reaction and a following annealing treatment. This hierarchical structure provides several advantages including a large contact surface area, short ion diffusion path and good charge transport, which are all beneficial for improving the electrochemical performance. As an integrated anode electrode in aqueous electrolyte, it delivers a high discharge capacity of ~2.13 mAh cm−2 (or ~304.30 mAh g−1) at a scan rate of 1 mV s−1, retains at ~1.68 mAh cm−2 at 10 mV s−1, and preserves ~88% of the initial capacity after 500 cycles. Combining our hierarchical Co3O4@Ni–Co–O nanoarray as the cathode electrode, we assemble a double hierarchical structured aqueous battery, which achieves an energy density and power density of ~2.1 mWh cm−2 and 42.8 mW cm−2, respectively. It also exhibits good cycling stability with a capacity of ~1.8 mAh cm−2 after 500 charge/discharge cycles.