Three-Dimensional graphene (3D-G) material is regarded as an excellent carbon material, which reveals cross-linked porous structure, high specific surface area, strong mechanical strength and high conductivity inheriting from the graphene. In this work, we fabricate the novel 3D-G based materials by decoration of sodium citrate (SC) for supercapacitor and lithium ion batteries (LIBs) applications. SC with abundant functional groups and short carbon chain can ensure the interface between graphene sheets or between graphene and other composite materials, lead to shorter diffusion path for ions transportation. Owing to the large surface area and pore volume, 3D-G (SC) shows outstanding specific capacitance (301 F g−1) when it is applied in supercapacitors. Besides that, 3D-G (SC) compounds with Fe3O4 particles and 3D-G@Fe3O4(SC) are applied in LIBs. The 3D-G@Fe3O4 (SC) has a higher discharge capacity (1310.6 mAh g−1) than 3D-G@Fe3O4 (1270 mAh g−1) at 0.1 C, and it even increase to an excellent capacity (1550 mAh g−1) after 100 cycles. Moreover, 3D-G@Fe3O4(SC) shows excellent cycling stability that specific capacity retains 1031 mAh g−1 after 1000 cycles. This work may extend a novel approach to prepare 3D-G electrode material for efficient storage devices.