A composite electrode with unique hetero-structure arrays was prepared by integration of Ni-Co-based mixed oxide NiCoO2 into 3D graphene supported by nickel foam (NiCoO2@rGO/NF). NiCoO2 arrays were directly grown on 3D graphene without any binder through a hydrothermal method. Further, the NiCoO2 arrays were composed of NiCoO2 nanowires on the surface of NiCoO2 ultrathin nanoflakes (nanoflakes@nanowires). Due to the unique hetero-structure arrays of NiCoO2 and the synergetic effect of NiCoO2/graphene, NiCoO2@rGO/NF shows higher specific capacitance of 1970 F g−1 than pure NiCoO2/NF (1569 F g−1). The capacitance retention of 102% (1732 F g−1) is maintained after 2500 cycles for NiCoO2@rGO/NF, while the NiCoO2/NF is only 61%. Furthermore, the effect of different hydrothermal time on the morphologies and capacitive performance of NiCoO2@rGO/NF was also investigated. The optimum hydrothermal time may be 6 h; the corresponding NiCoO2@rGO/NF-6h shows the highest capacitance and best rate capability. Therefore, the reasonable combination of nanowires and nanoflakes can further enhance capacitance of NiCoO2. The asymmetric supercapacitor prepared by NiCoO2@rGO/NF and graphene/NF exhibits a maximum energy density of 42.3 Wh kg−1 at power density of 0.4 kW kg−1. This work also shows that NiCoO2@rGO/NF with hetero-structure arrays has great promise in supercapacitor with high energy density.