In order to reduce the volume, weight and cost of conventional hybrid energy storage system (HESS) while properly exploring the complementary features of different energy storage devices for DC microgrid applications, this paper proposes a multiple-port three-level DC/DC converter. It possesses multiple ports sharing one front-end three-level DC/DC converter with an inductor and supercapacitor bank. Different types of batteries and/or multiple battery banks can be interfaced through the multiple terminals. Such a converter structure facilitates the cooperation of different energy storage devices to satisfy various power demands of DC microgrids with intermittent renewable generation plants. Moreover, the proposed structure allows power sharing among different energy storage devices, which enables more efficient cooperation of different battery banks or different types of batteries. Experimental results are presented to verify the efficacy of the proposed converter structure and its control.