In order to study the safe and high-efficiency intelligent charging method for electric vehicle, the improved energy conservation SOC estimation algorithm which considers the effects of the battery capacity attenuation and the internal resistance loss on the SOC estimation is proposed. The improved SOC estimation algorithm was based on the traditional energy conservation method. Then, in order to verify the accuracy and feasibility of estimation algorithms, the above proposed improved SOC estimation algorithm was analyzed and compared with the traditional charging methods. Furthermore, according to the optimal charging current with Maas Theorem, the three-stage intelligent charging method (small current charging, pulse charging and constant voltage charging) was proposed based on the improved energy conservation SOC estimation algorithm,and the three-stage intelligent charging simulation model based on the improved energy conservation SOC estimation algorithm was established. The simulation results showed that the SOC value obtained by the improved energy conservation SOC estimation algorithm was smaller than the value obtained by the traditional energy conservation method. And the SOC value obtained by the improved energy conservation SOC estimation algorithm was more close to the real SOC value. Moreover, the three-stage intelligent charging method based on the improved energy conservation SOC estimation algorithm can intelligently select the detailed charging method according to the SOC variation, which could realize the fast and safe charging for electric vehicle. The proposed three-stage intelligent charging method can provide reference for current charging method study for electric vehicle. And the improved SOC estimation algorithm can also provide one feasible method to enhance the effectiveness of the intelligent charging method for electric vehicle. In addition, three-stage intelligent charging method can lay the foundation for application of the intelligent charging theory to engineering practice.