Si has a very high theoretical capacity of 4200 mAh g−1 as the anode materials for lithium ion batteries, which is near ten times higher than that of the current commercial graphite anode. However, it suffers from severe volume expansion/contraction during the charge/discharge processes, which is the main obstacle for its application. In this work, we prepare Si/C composite anodes with an intercalated Si/C multilayer structure by alternately depositing C and Si by plasma decomposition of C2H2 and magnetron sputtering of a Si target, respectively. Near theoretical capacity can be achieved (about 4000 mAh g−1) for more than 100 cycles for thin Si layers, which is attributed to the buffer effect of the carbon layers. This structure is also scalable up to multiple Si/C layers. A critical thickness of 20 nm is found for the silicon layer, below which the near theoretical capacity can be stably maintained. This critical thickness may shed light on future designs of nanostructured silicon anode with high capacity and stability for lithium ion batteries.