Highly ordered mesoporous Si/C (OMP-Si/C) anode composite for lithium ion battery is fabricated by a moderate magnesiothermic reduction and carbon coating using SBA-15 as a precursor. The synthesized OMP-Si/C composite rods preserve the original nanostructure of ordered honeycomb pore channels in SBA-15 and link one by one to form lotus-root-like chains which tightly agglutinate into bundles with a high packing density. A liquid ambient reaction model is also proposed to describe the reaction mechanism between SBA-15 and magnesium powder and the formation of this unusual highly ordered mesoporous structure at temperature of 660°C. The samples are characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, nitrogen adsorption, and Raman spectroscopy. The highly ordered mesoporous structure provides buffering space to accommodate the large volume expansion/contraction and consequent stress induced inside silicon during Li+ insertion/extraction. Furthermore, this mesoporous structure can also provide transportation routes for electrolyte and shorten the diffusion paths for lithium ions. The carbon coating on mesoporous silicon can provide electronically conductive networks for the electrode. These effectively mitigate silicon pulverization issue and help achieve higher reversible capacity and better capacity retention. The excellent electrochemical performance of this highly ordered mesoporous Si/C shows its promising applications in anode materials for Li-ion batteries.