A three-level dual active bridge (3L-DAB) DC-DC converter with the introduction of 3L legs is applied to the bidirectional charging stack in a charging station, so that the system’s regulating flexibility can be enhanced by adding another control degree of freedom. When the conventional phase shift (CPS) control is adopted, the current stress of the 3L-DAB converter is relatively large, which increases the loss and thus reduces the system efficiency. To address this issue, an optimal control strategy is proposed to minimize the current stress of the DC-DC converter applied to the bidirectional charging stack. First, the mathematical model of the 3L-DAB converter under phase shift control is established to analyze the relationship between the harmonics of inductance current RMS and the control degrees of freedom. On this basis, a control strategy based on fundamental wave optimization is put forward to reduce the inductance current of the converter. Finally, the correctness of theoretical analysis and the effectiveness of the proposed control strategy are verified by comparing the simulation and experimental results among the proposed optimal control and other control methods.