Nanostructured Co3O4 materials attracted significant attention due to their exceptional electrochemical (pseudo-capacitive) properties. However, rigorous preparation conditions are needed to control the size (especially nanosize), morphology and size distribution of the products obtained by conventional methods. Herein, we describe a novel one step shape-controlled synthesis of uniform Co3O4 nanocubes with a size of 50 nm with the existence of mesoporous carbon nanorods (meso-CNRs). In this synthesis process, meso-CNRs not only act as a heat receiver to directly obtain Co3O4 eliminating the high-temperature post-calcination, but also control the morphology of the resulting Co3O4 to form nanocubes with uniform distribution. More strikingly, mesoporous Co3O4 nanocubes are obtained by further thermal treatment. The structure and morphology of the samples were characterized by scanning electron microscopy, transmission electron microscopy and X-ray diffraction. A possible formation mechanism of mesoporous Co3O4 nanocubes is proposed here. Electrochemical tests have revealed that the prepared mesoporous Co3O4 nanocubes demonstrate a remarkable performance in supercapacitor applications due to the porous structure, which endows fast ion and electron transfer.