A unique composite nanonet of metal oxide@carbon interconnected sheets is obtained by atomic layer deposition (ALD)-assisted fabrication. In this nanonet structure, mesoporous metal oxide nanosheets are covered by a layer of amorphous carbon nanoflakes. Specifically, quasi-vertical aligned and mesoporous Ni(x)Co(1-x)O nanosheets are first fabricated directly on nickel foam substrates by a hydrothermal method. Then, an ALD-enabled carbon coating method is applied for the growth of carbon nanoflakes on the surface of the nanosheets. The thus formed 3D hierarchical structure of Ni(x)Co(1-x)O@carbon composite flakes have a higher surface area, better electrical conductivity and structure stability than the bare Ni(x)Co(1-x)O. The application of such composite nanomaterials is demonstrated as electrodes for a supercapacitor and a lithium-ion battery. In both tests, the composite electrode shows enhancement in capacity and cycling stability. This effective composite nanostructure design of metal oxides@carbon flakes could provide a promising method to construct high-performance materials for energy and environment applications.