A hybrid‐three‐level isolated dual‐active‐bridge (HTDAB) DC–DC converter is widely used for grid‐interactive power converters. However, a traditional extended‐phase‐shift (EPS) modulation scheme would cause voltage‐level‐disorder (VLD) problems in HDAB DC–DC converter system because the output voltage of HTDAB would be clamped at a high‐ or low‐level during power transmission when the inductor current changes directions. Thus, the zero voltage sequence of the HTDAB cannot be stably maintained under EPS control, which not only leads to a significant difference between the actual transmission power and the target output power but also seriously affects the stability of the system control. To address this limitation, the reasons leading to VLD are analysed in detail, that is, an inappropriate PWM switching sequence at the output zero voltage level would occur under EPS control. Then, a novel PWM plus phase shift (PPS) modulation strategy is proposed, which can eliminate VLD completely. Finally, an experimental prototype is built to verify the effectiveness of the proposed PPS modulation scheme. The experimental results demonstrate that the PPS modulation method proposed in this article can effectively eliminate level disturbances and improve system stability.