As the important indices for reflecting the comprehensive performance of the battery, the parameters of lithium-ion are unavailable by direct observation. Through identifying internal circuit parameters by establishing multiple linear regression model, a new method for the state of charge estimation of lithium-ion batteries by indirectly observing the batteries balance electromotive force was proposed. The equivalent capacitance was introduced to represent capacity character of lithium-ion batteries in this new method, which was based on an improved Thevenin battery model. Through measuring changes of open-circuit voltage and charge before and after the discharge process in a cycle period, the equivalent capacitance can be recognized in a long time scale. As the main variable for estimating state of charge, the balance electromotive force can be dynamically estimated through the equivalent capacitance in a short time scale. Finally, a pulse discharging experiment of a cycle period verified the effectiveness and accuracy of the improved battery model and the proposed dynamic identification method.