In this paper, an isolated three-level H-bridge DC/DC converter has been designed, which is the core device of the DC zonal electrical distribution module (DC-ZEDM) in the new-generation medium-voltage DC vessel integrated power system (IPS). It supplies isolated low-voltage DC to the second-level converter of DC-ZEDM. Considering the problem of relatively large size and weight of a transformer working at a frequency of 50Hz, the phase-shift PWM was used for controlling the converter to increase its frequency and decrease the size and weight of the transformer. And this paper has analyzed the harmonic waves of the H-bridge's output voltage and presented the static operating point at which all the operating modes in one switching period are under CCM. For the loss of duty ratio due to leakage induction, an appropriate compensation solution has been proposed. Finally, a 20kW, 1kHz prototype was applied to the verification of the operating principle of the converter.