Flying-capacitor multiplexed modulation technology is suitable for bipolar DC microgrids with higher voltage levels and higher current levels. The module combination and corresponding modulation method can be flexibly selected according to the voltage level and capacity level. This paper proposes a bipolar bidirectional DC/DC converter and its interleaved-complementary modulation strategy that is suitable for bipolar DC microgrids. The converter consists of two flying-capacitor three-level bidirectional DC/DC converters that are interleaved in parallel 90°, and then cascaded with another module to form a symmetrical structure of the upper and lower arms; the complementary modulation of the upper and lower half bridges constitutes an interleaved complementary multilevel bidirectional DC/DC converter. If the bidirectional converter needs to provide a stronger overcurrent capability, more bridge arms can be interleaved in parallel. Once n bridge arms are connected in parallel, the bridge arms should be interleaved 180°/n in parallel. In bipolar DC microgrids, the upper and lower arms should be complementarily modulated, and the input and output are isolated by the inductance. To solve the current difference, caused by the inconsistent parasitic, the voltage-current double closed-loop-control is used, and the dynamic response is faster during bidirectional operation. This paper proposes theoretical analysis and experiments that verify bipolar bidirectional DC/DC converter for high-power energy storage.