In DC micro-grid system energy storage systems (ESS) are responsible for storing energy and balancing power. Also, control target of the bidirectional DC-DC converter(BDC) for ESS should be changed depending on the operating mode. During the grid connected mode, the BDC controls the battery current or voltage. When a grid fault occurs, the BDC should change the control target to regulate the DC-bus. The BDC with conventional control method may experience large transient state during the mode change. This paper proposes a control method of BDC for ESS. The proposed control method is able to provide autonomous and seamless mode transfer by a variable current limiter. To validate the proposed concept, simulation results using PSIM and experimental results from a 2kW prototype are provided.