Porous hierarchical nanostructures have received wide attention in high-performance lithium ion batteries (LIBs) applications. In this work, we report a simple strategy for the fabrication of porous Co/Co3O4–C core-branch nanowire arrays. By the aid of chemical bath deposition, electro-deposition and annealing process, Co3O4–C nanoflake branch is successfully assembled on the Co core nanowires forming the aligned core-branch nanowires with diameters of about 550 nm. As anode materials for LIBs, the Co/Co3O4–C core-branch nanowire arrays exhibit high reversible capacity, improved cycle stability as well as good rate capability. A specific capacity of 608 mAh g−1 is obtained at 0.5C after 200 cycles, much higher than the unmodified Co3O4 nanoflake arrays (501 mAh g−1 at 0.5C after 200 cycles). The enhanced electrochemical properties are mainly ascribed to the porous core-branch architecture with faster ion/electron transfer path. This newly developed method can be extended to prepare other advanced core-branch nanomaterials for applications in electrochemical and optoelectronic devices.