A new three-level bidirectional DC-DC converter configuration for the battery and supercapacitor (SC) energy storage systems in DC microgrids is presented in this paper. The PI-based control method is implemented to operate the proposed converter with hybrid energy storage system. Furthermore, joint control is utilized to obtain rapid DC-link voltage restoration and effective power sharing between battery and SC based on their respective characteristics. The system operating principle, controller design, stability analysis, simulation studies and experimental studies are presented in this paper. The proposed three-level bidirectional DC-DC converter configuration can effectively integrate the battery and SC with the bidirectional power flow. The proposed control method provides the effective participation of the SC system which reduces the stress on the battery system. The presented converter configuration is effective in reducing the stress on the power semiconductors and provides better performance with smaller passive components. The experimental platform is built to test and validate the three-level bidirectional DC-DC converter and proposed control method for the HESS.