Multi-level dual active bridge (MLDAB) bidirectional DC-DC converters often encounter harmonic issues in the high-frequency link (HFL) during power conversion, irrespective of the modulation scheme employed. These harmonics in the HFL inductor current result in elevated RMS current, thereby increasing current stress on the switching devices. Furthermore, the presence of harmonics leads to higher operating temperatures in the high-frequency transformer (HFT) and other associated components, ultimately compromising system efficiency. To address the limitations of conventional MLDAB converters, this paper proposes a novel topology incorporating sextuple phase shift modulation (SPSM) based MLDAB converter. The proposed approach significantly reduces the harmonic content in the HFL inductor current, leading to lower power losses and improved overall efficiency. Further, this paper provides a comparative evaluation against the conventional quintuple phase shift (QPS) modulation based MLDAB converter. The results demonstrate that the proposed topology with novel modulation based MLDAB converter effectively minimizes harmonics in the HFL inductor current and delivers higher efficiency compared to the conventional modulation based MLDAB converter. This makes the proposed topology with novel SPSM based MLDAB converter a superior solution for DC-DC converter applications. Also, the results of the proposed MLDAB converter has been validated through real-time results using an OPAL-RT hardware-in-the-loop emulator.