In this work, a series of metal oxide double-layer nanospheres (DLNs), such as Mn2O3, Co3O4, NiO, NiCo2O4, and MnCo2O4 have been successfully synthesized through a general template method. The layers of nanospheres were assembled by different nanostructure units and the removing of the SiO2 template formed a void of several ten nanometers between the double layers, resulting large specific surface areas for them. The energy storage performances of the as-prepared double-layer nanospheres were further investigated in lithium ion battery and supercapacitor systems. Based on their unique nanostructures, the double-layer nanospheres exhibit excellent electrochemical performance with long cycle stability and high specific capacities or capacitances. The best of these, DLNs-NiCo2O4 can deliver a reversible capacity of 1107mAhg−1 at 0.25C after 200 cycles in lithium ion battery system, and shows a capacitance of 1088Fg−1 with capacitance loss of less than 3% at 5Ag−1 after 5000 cycles in supercapacitors.