Reasonable selection of carbon-based buffer materials is of great importance to improve the lithium storage performance of alloy-based anode materials. In this work, two Sn/C nanocomposites with almost identical Sn/C ratio but different carbon structures, namely Sn/amorphous carbon (Sn/C-a) and Sn/graphitized carbon (Sn/C-g) multilayers, are prepared by a home-made tandem plasma reactor and are contrasted for their lithium storage performance. Lithiation/delithiation behaviors of the two samples are intensively studied by cyclic voltammery, galvanostatic intermittent titration technique and electrochemical impedance spectroscopy. The results imply that the multilayer Sn/C-a electrode exhibits better lithium ion diffusion kinetics than the Sn/C-g electrode during the initial few cycles. However, the Sn/C-g electrode possesses better structure robustness because of the good electric and mechanical properties of the graphitized carbon, which results in higher cyclic stability than the Sn/C-a electrode, featured for a high capacity of 898 mA h g−1 after more than 500 cycles at a current density of 100 mA g−1.