Novel high performance active electrode materials for green energy-storage systems attract great interest in the past decades. Here, for the first time, 3D mesoporous flower-like CuCo2S4/CuCo2O4 heterostructure with compatible nanoscale interfaces and tunable chemical composition is designed and prepared. Because of the unique architecture and components, the electrode exhibits large electrochemical surface area, enhanced conductivity, short ion diffusion path, and rapid electron and ion transport rate, resulting in its outstanding electrochemical properties of specific capacity (599.9C g−1), excellent cycling stability and high rate capability. An asymmetric supercapacitor device based on these unique nanoflowers as cathode and graphene aerogel as anode delivers substantial energy density (33.2 W h kg−1), power density (13.3 kW kg−1), and high long-term stability (73% capacitance retention after 10000 cycles). These results imply great potential application in high-performance supercapacitors.