Lithium ion capacitors are assembled with pre-lithiated mesocarbon microbeads (LMCMB) anode and activated carbon (AC) cathode. The effect of pre-lithiation degrees on the crystal structure of MCMB electrode and the electrochemical capacitance behavior of LIC are investigated by X-ray diffraction (XRD) and the charge-discharge test of three-electrode cell. The structure of graphite still maintained when the pre-lithiation capacity is less than 200 mAh g−1, phase transition takes place with the increase of pre-lithiation capacity from 250 mAh g−1 to 350 mAh g−1. Pre-lithiation degrees of MCMB anode greatly affect the charge-discharge process and behavior, which impact on the electrochemical performance of LIC. The LIC with pre-lithiation capacity of 300 mAh g−1 has the optimal electrochemical performance. The energy density of LIC300 is up to 92.3 Wh kg−1, the power density as high as 5.5kWkg−1 and the capacity retention is 97.0% after 1000 cycles. The excellent electrochemical performance benefits from the appropriate pre-lithiation capacity of negative electrode. The appropriate pre-lithiation ensures the working voltage of negative electrode in low and relative stable charge-discharge platform corresponding to the mutual phase transition from the second stage graphite intercalation compound (LiC12) to the first stage graphite intercalation compound (LiC6). The stable charge-discharge platform of negative electrode is conductive to the sufficient utilization of AC positive electrode.