In this paper, we report on the preparation of Si–Y multi-layer thin films by magnetron sputtering and their application as anode materials of lithium-ion batteries. Scanning electron microscopy (SEM) with energy dispersive X-ray (EDX) and transmission electron microscopy (TEM) have been used to characterize the morphologies and structures of the as-prepared thin films. The framework of the Si–Y thin films is Y-Si-Y-Si multi-layers, including the Si thin film with a thickness of 225nm and the Y thin film with different thickness (15–37.5nm). The electrochemical performance of the samples is investigated by charge–discharge measurement, cyclic voltammetry and electrochemical impedance spectra (EIS). Compared with pure Si thin film, the Si–Y thin films with the optimal Y film thickness of about 22.5nm can deliver a high reversible capacity of 2450mAhg−1 under a current density of 0.4C after 50 cycles, showing superior cycle performance and electrode stability due to the better Li+ diffusion character. This study should shed light on the design and application of Si–Y multi-layer thin films as anode materials of high-capacity lithium-ion batteries.