The combination of silicon and carbon layer exhibited superior lithium capacity and rate performance, however, the corresponding lithiation mechanism in atomic scale is not clear. In this work, the electrochemical performance of silicon anode incorporated with carbon layer is evaluated by first principles calculations. The average length of Li-Si bond near the silicon-carbon interface is significantly shorter than that in silicon, indicating an irreversible capacity loss. The reversible lithium capacity is then calculated by excluding the lithium atoms with shorter Li-Si bonds. A reversible capacity of 2197 mAhg(-1) is predicted and is comparable to the reversible capacity of 2509 mAhg(-1) in experiment. Moreover, the silicon-carbon structure corresponds to enhanced electronic conductivity and lithium diffusion coefficient compared to silicon, resulting in excellent rate capability as revealed in experiments.