It is considered that the dynamic performance of super capacitor and battery hybrid energy storage system is poor and the output waveform of AC voltage distorts seriously. The third harmonic injection PWM (THIPWM) with the three-level inverter, which has an excellent performance to improve the dynamic performance of the super capacitor and battery, gathers information from ends of the DC output voltage or current and the total current of the DC side to solve the problem of unbalanced neutral line voltage of three-level inverter. It also keeps super capacitor and battery controlled smoothly during the operation, and reduces the final output waveform distortion index. The Matlab simulation model is established and the results verify the practicality and correctness of the three-level inverter topology and its control algorithm.