Three-dimensional (3D) architectures of graphene derivatives have attracted intensive attention due to their outstanding electric conductance and unique interconnected huge surface area. It is expected to transfer these excellent properties of 3D graphene into microsystems for further development in the microelectronic industry. However, limited applications are reported due to the absence of suitable fabrication approaches of 3D graphene that are compatible with existing silicon-based microfabrication techniques. In this paper, a novel 3D hierarchical graphene was prepared using a plasma-enhanced chemical vapor deposition to synthesize graphene nanoflakes on silicon nanowires (SiNWs) scaffolds that are generated from metal-assisted chemical etching (MACE). In addition to the first growth mechanism study of graphene on different substrates, the application of 3D graphene derivatives was further explored towards energy storage through an electrochemical evaluation. The 3D graphene electrode, combined with pseudocapacitive polyaniline coating, showed a large specific capacitance of 185 mF cm− 2, which outperforms its planar counterparts and is desirable for constructing micro-supercapacitors towards chip-scale power supplying. Above all, this microfabrication strategy of 3D graphene on high aspect ratio silicon nanostructures can also be extended as a platform toolkit towards the application of micro-batteries, solar cells and sensors in microsystems.