We propose an autonomous DC microgrid system in which a three-way isolated DC/DC converter is used as a power routing unit. As the unit in the system operates with various power flow patterns, a highly efficient system cannot be easily designed unless the dependence of the unit's overall loss on the flow pattern is suppressed and efficiency variations in any operational state are small. We made a prototype three-way isolated DC/DC converter consisting of SiC-MOSFETs rated at 400 V, 20 kHz, and 10 kW and demonstrated power distribution operation. In this paper we present the dependence of overall loss in the three-way converter as revealed by results of experiments and we analyze the factors involved in this dependence. We also propose a design approach to suppressing the dependence of overall loss on power flow pattern.