It is important to estimate State Of Charge (SOC) of rechargeable batteries for electric vehicles. To estimate SOC accurately, it is required to construct a model that can capture the dynamics of batteries and predict their behavior with sufficient accuracy. However, conventional system identification techniques cannot take into account the characteristics of batteries such as relationship of SOC and Open Circuit Voltage (OCV) and diffusion phenomena. To address such an issue, this paper proposes an estimation method of parameters in the model that reflects the characteristics of batteries using continuous-time system identification technique. This method can achieve high accuracy in the parameter estimation. Its effectiveness is examined through numerical simulations and an experiment under the electric vehicle operating environment.