The isolated modular multilevel DC transformer (iM2DCT) possesses high scalability and modularity, making it a key device for connecting energy storage systems to medium-voltage DC (MVDC) distribution networks. However, voltage fluctuations on the energy storage side could disrupt the unity voltage conversion ratio, leading to submodule (SM) capacitor voltage imbalance. Existing methods are unable to address the SM capacitor voltage imbalance of iM2DCT under non-unity voltage conversion ratio scenarios. To solve this issue, this article proposes a strategy by redistributing the SMs’ phase shift pulses. The effectiveness and feasibility of this method are validated through a full-power simulation model in MATLAB.