A flux-balancing method for an isolated bidirectional converter uses a flux-balancing control loop and a current-balancing control loop to control the DC components in the primary and secondary currents. The flux-balancing control loop keeps the average magnetizing current substantially zero and the current-balancing control loop keeps the average primary current or the average secondary current substantially zero. The flux-balancing loop adjusts the duty ratio of a set of switches in a corresponding bridge. The adjusted duty ratio is designed to substantially eliminate the DC component in the magnetizing current. The current-balancing loop keeps the average primary current and the average secondary current substantially zero, and adjusts the duty ratio of the switches in a corresponding bridge to eliminate the corresponding DC component.