A facile method for preparing mesoporous perforated Co3O4 nanoparticles with hollow channels and a thin carbon layer was newly designed and achieved with sacrificial carbon nanotube (CNT) templates. The threaded Co3O4 nanoparticles on the CNTs were fabricated through a hybridization process, and a subsequent calcination process produced mesoporous perforated Co3O4 nanoparticles. With a finely tuned calcination, CNTs were sacrificed to generate hollow channels in the Co3O4 nanoparticles and to provide a carbon source for the formation of a few nm-thick carbon layer on the surface of the Co3O4 nanoparticles simultaneously. The prepared mesoporous perforated Co3O4 nanoparticles with a robust electronic conductive layer enabled not only an enhanced electrochemical reactivity from the greatly increased contact area between the electrolyte and electrode but also a high electronic conductivity of the overall electrode so that excellent electrochemical performances (1115.1 mA h g−1 after 100 cycles; 595.9 mA h g−1 @ 5 C rate) were successfully achieved in the anode application of a lithium-ion battery.