This paper deals with the problem of estimating the state of charge (SOC) of lithium-ion batteries. Based on the analysis of the impedance spectra obtained by electrochemical impedance spectroscopy (EIS), a simplified battery impedance model is derived with the constant phase element (CPE). To interpret the impedance model, a fractional order calculus (FOC) method is introduced to model the CPE in the impedance model. A new identification method is proposed to identify the impedance model, considering both accuracy and simplicity. The fractional Kalman filter is introduced to estimate the SOC of the lithium-ion battery based on the impedance model. Finally, a battery test bench is established, and the proposed method is verified by a scaled down system on the urban dynamometer driving schedule (UDDS) drive cycle test.