Graphene-based nanocomposites have been synthesized and tested as electrode materials for high power lithium-ion batteries. In the synthesis of such nanocomposites, graphene is generally introduced by either thermally or chemically reduced graphite oxide (GO), which has poorer electric conductivity and crystallinity than mechanically exfoliated graphene. Here, we prepare few-layer graphene sheet (FLGS) with high electric conductivity, by sonicating expanded graphite in DMF solvent, and develop a simple one-pot hydrothermal method to fabricate monodispersed and ultrasmall Co3O4 nanocubes (about 4 nm in size) on the FLGS. This composite, consisting of homogeneously assembled and high crystalline Co3O4 nanocubes on the FLGS, has shown higher capacity and much better cycling stability than counterparts synthesized using GO as a precursor. The products in different synthesis stages have been characterized by TEM, FTIR and XPS to investigate the nanocube growth mechanism. We find that Co(OH)2 initially grew homogeneously on the graphene surface, then gradually oxidized to form Co3O4 nanoparticle seeds, and finally converted to Co3O4 nanocubes with caboxylated anion as surfactant. This work explores the mechanism of nanocrystal growth and its impact on electrochemical properties to provide further insights into the development of nanostructured electrode materials for high power energy storage.