Rational design of carbon based binary composites is of critical importance to improve the performance of alloy type anode materials in lithium ion batteries. In this work, two thin film Sn-C electrodes with similar Sn/C ratio but distinct nanostructures, namely carbon coated core-shell structure and alternating Sn/C multilayers, are prepared by direct plasma deposition in a tandem plasma reactor and are compared for their performance as anode materials for lithium ion batteries. Lithiation/delithiation behaviors of the two samples are comprehensively studied by cyclic voltammetry, galvanostatic intermittent titration technique and electrochemical impedance spectroscopy. The results suggest that the core-shell Sn@C electrode is more favorable for Li+ transport and the interface charge transfer, which leads to higher cyclic stability and rate performance than the alternating Sn/C multilayer electrode, featuring for a high capacity of 849 mAh g−1 (0.083 mAh cm−2) after more than 600 cycles at a current density of 100 mA g−1 (0.01 mA cm−2) and a high capacity of 500 mAh g−1 (0.049 mAh cm−2) at high current density of 2000 mA g−1 (0.2 mA cm−2).