We have successfully synthesized the amorphous silicon/carbon (a-Si/C) multilayer thin films by magnetic sputtering method. The bonding characteristics and phase identification were investigated by X-ray diffraction (XRD) and Raman spectrum. The electrochemical performance of the a-Si/C multilayer thin films as anode materials for lithium ion batteries showed that with various thicknesses of Si layers, the electrodes displayed huge differences on the reversible capacity and cycling stability. The 500 nm a-Si/C multilayer films, with the thickness ratio d Si:d C = 5:1, displayed a high reversible capacity of about 2000 mA h g−1 over 200 cycles at 1C rate and a best structure integrity at various charging/discharging rates test. The micro-scale a-Si/C multilayer thin films (1.1 μm) also showed a good cycling performance with a capacity of about 1900 mA h g−1 at a current density of 2000 mA g−1 over 200 cycles.