The porous carbon nanotubes were selectively prepared from the pristine carbon nanotubes. The surface of carbon nanotubes was firstly functionalized with Fe2O3 nanoparticles and subsequent heat treatment induced CNT etching. After removal of Fe2O3 nanoparticles, mesopores were formed in carbon nanotubes and thus porous structure was obtained. The obtained material of porous carbon nanotubes with higher specific surface area and larger pore sizes was tested as anode material of lithium ion batteries and showed improved performance with respect to the pristine carbon nanotubes.