Mesoporous silicon nanorods assembled by small nanocrystals were successfully prepared using multi-walled carbon nanotubes (MWCNTs) as a template via a facile magnesiothermic reduction process. The obtained product was characterized by X-ray diffraction, Raman spectroscopy, transmission electron microscopy, nitrogen adsorption-desorption measurement and electrochemical measurements. The resulting mesoporous silicon nanorods as an anode exhibit a significantly improved electrochemical performance compared with the porous silicon networks and bulk silicon. The reversible capacity can retain 1038mAhg−1 at 200mAg−1 after 170 cycles. Even at a high rate of 2000mAg−1, a reversible capacity of 664mAhg−1 can still be obtained. All these results suggest that the mesoporous silicon nanorods are a promising candidate for the next generation of lithium ion batteries.