Modified natural graphite was prepared by impregnation method with alkali as surface modification agent. X-ray diffraction (XRD), Fourier transform infrared spectrometer (FTIR), Land battery test system (Land) and Electrochemical workstations were used to characterize the structure, charge–discharge performances and AC impedance properties of samples. XRD results show that alkali treatment improves the graphitization degree of natural graphite because La and Lc increase. FTIR tests show that alkali treatment changes the surface chemistry of the natural graphite because aldehyde group is detected at 2950–2800 cm−1 and carboxylic acid group peak is enhanced at 1700–1600 cm−1. Charge–discharge performances reveal that cycle performance and rate capacity are improved in the case of NaOH. The lithium-deinsertion capacity of NGNa3, NGLi3 and NG are, respectively, 324.8 mAh g−1, 313.2 mAh g−1 and 299.9 mAh g−1, and capacity retention rate are 95.2%, 90.0% and 86.8% after 20 cycles at 0.5 C, separately. The mechanism of the enhancement were investigated by AC impedance, as a result of which, the membrane resistance RSEI and charge transfer impedance Rct decrease, and membrane capacitance CSEI and extracted capacitance CCPE increase. It indicates that the preformation of SEI by alkali treatment could be beneficial to the decrease of RSEI, which could prevent the co-intercalation of solvent molecules and be contributed to the good cycle performance. In addition, from the increase of capacitance, we infer that modified natural graphite surface become coarse and more micropores, and thus, more sites are provided for lithium intercalation and de-intercalation.