Compared to the AC counterpart, the DC shore power system provides a significant advantage of efficient power supply from renewable sources to ships and onshore loads. Super-capacitors serve as key energy storage units in such a system to buffer the power fluctuations and collect the regenerative energy. However, the ultra-wide voltage range of super-capacitors imposes a significant challenge in the topology selection and efficiency optimization of the interfacing isolated bidirectional DC–DC converter. To tackle this challenge, this paper analyzes and compares two promising converter topologies, which are a configurable modular two-level dual-active bridge (CM-2L-DAB) and a three-level dual-active bridge (3L-DAB). To facilitate an ultra-wide voltage range, extended phase-shift (EPS) modulation in conjunction with the topology reconfiguration is analyzed for the CM-2L-DAB, while a hybrid modulation scheme is proposed for the 3L-DAB. A unified design approach is provided for both topologies, which also yields to the power loss modeling. On this basis, the CM-2L-DAB and 3L-DAB are thoroughly compared in terms of the modulation schemes, current stress, soft-switching operation, power conversion efficiency, material usage, closed-loop control scheme, and reliability. A prominent conclusion can be drawn that the CM-2L-DAB provides a higher efficiency than the 3L-DAB over the whole voltage range, but it relies on additional relays to reconfigure its topology which results in lower reliability and dynamic performance than the 3L-DAB.