The invention discloses a novel two-stage bidirectional energy storage converter control system and a control method thereof. An energy storage converter main circuit mainly comprises a three-phase voltage type PWM (Pulse Width Modulation) rectifier, a novel half bridge three-level push-pull bidirectional DC-DC converter, a charging-discharging buffer interface circuit for limiting battery charging current, and a battery pack module. A control system circuit mainly comprises a voltage and current sensor, a driving circuit, a protection circuit, a main controller, an SOC (State of Charge) detection module, a radiator, a buzzer, a man-machine interface, a communication interface circuit and a system auxiliary power supply. The alternating-current micro-grid power or voltage and the states of charge of energy storage batteries can be detected in real time, so that the running modes of each generating set and the energy storage converter in a micro-grid system are controlled flexibly, and the effects of 'filling peaks and clipping valleys' in a power system, smoothening power in a wind-solar hybrid micro-grid system and the like are achieved. Moreover, the control system has the advantages of high power density, small size, high efficiency, low harmonic content, high reliability, high self-control degree and the like.