The hollow mesoporous silicon nanobox dually encapsulated by tin oxide and carbon layers is successfully fabricated and used for anode active material of lithium ion battery. The effects of the double coating layers on the structure, morphology and features of nanocomposite are systematically investigated by transmission electron microscopy, field emission scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and galvanostatic charge-discharge tests. The results reveal that hollow mesoporous silicon/tin oxide/carbon nanobox has the adjustable void space and a rationally designed hierarchical structure, which permits the free expansion of Si core without breaking double coating layers and preserves the structural integrity of the electrode during the (de)lithiation processes, as well as significantly enhances the electronic conductivity of anode. As expected, the resultant hollow mesoporous silicon/tin oxide/carbon nanobox exhibits a high reversible capacity up to 1535 mAh g−1 at 0.5 A g−1 after 200 cycles of (dis)charging due to the unique nanostructure. Especially, the as-synthesized nanocomposite exhibits an excellent rate capacity as high as 858 mAh g−1 at 6 A g−1. This rational structure design and innovative approach can be of visible significance for the development of new anode active materials of next-generation lithium-ion battery.