Reasonable design and fabrication of free-standing nano-composite architecture is significant for their applications in electrochemical energy storage such as lithium ion batteries (LIBs). In this work, Co3O4 nanoparticles (NPs) encapsulated in a well-aligned carbon nanowire array on a 3D Ni-foam is successfully designed and fabricated by using the Co2(OH)2(CO3)2 nanowires as templates and followed by surface glucose polymerization and two step annealing treatment. When used as a free-standing anode in LIBs, the Co3O4 NPs/carbon nanowire composite exhibits an enhanced lithium storage performance with a higher reversible capacity, better cycling stability and rate capability compared with bare Co3O4 nanowires and NPs. This work is valuable for the design of future free-standing electrodes for electrochemical applications.