The invention relates to a battery energy storage system based power conversion system and a control method thereof. The power conversion system comprises a battery energy storage system, a bidirectional DC/DC (direct-current) converter, a grid-side current transformer, a filter circuit and an isolated voltage transformer. The battery energy storage system is in parallel connection with a direct-current bus of the grid-side current transformer through the bidirectional DC/DC converter; the grid-side current transformer, the filter circuit and the isolated voltage transformer are connected in sequence; and the isolated voltage transformer accesses to a power grid. The control method includes sequentially monitoring the battery energy storage system, the bidirectional DC/DC converter, the grid-side current transformer, the filter circuit and the isolated voltage transformer by a control circuit. Since the battery energy storage system utilizes battery cells connected in series and is in parallel connection with the common direct-current bus through the bidirectional DC/DC converter, circulation among battery packs is avoided, and capacity expansion of the system is facilitated. Further, by the aid of the monitoring control strategy for SOC (super capacitor state of charge) of the battery energy storage system and battery end voltage, excessive charge or discharge state of the battery energy storage system is avoided, service lives of the battery packs are prolonged, and comprehensive service cost is lowered.