The modular multilevel converter–bidirectional DC–DC converter (MMC–BDC) has been proposed to be utilized in the vessel integrated power system to interconnect the medium voltage bus and the distributed energy storage elements. In the shipboard applications, MMC–BDC faces unbalanced sub-module power operation because of the inconsistent state-of-charge (SOC) of the energy storage elements. Researchers have investigated into the unbalanced operation principle of MMC–BDC and proposed some unbalanced operation control strategies, but these traditional strategies do not perform well in both aspects of operating range and efficiency. Therefore, this paper proposes a novel Lyapunov-function-based feedback linearization control strategy for the independent sub-module voltage control of MMC–BDC, which not only shows wide unbalanced operation range and high efficiency, but also realizes the decoupling and symmetrical control of the sub-module capacitor voltages.