A study for heave compensation system of super capacitor energy storage devices, which uses the bidirectional DC/DC converter for connecting DC bus and super capacitor, and aims at solving problems of heave compensation feedback electricity use. The three-phase half bridge of isolated bi-directional DC/DC converter as the transmission circuit with the change of the DC bus voltage as reference is selected, the double closed loop control strategy of bidirectional DC/DC converter is designed, for achieving stability of bus bar voltage. As the DC bus voltage rises, super capacitor is charged; as the DC bus voltage reduces, the super capacitor is discharged. Experiments verify the effectiveness of the control strategy for the proposed bidirectional DC/DC converter based on DSP of super capacitor energy storage device.