Dual Three-phase motor drives offer significant advantages over conventional three-phase motors. However, the stator resistance and leakage inductance are the only harmonic impedance, so they are easily occurring large stator current harmonics. This paper proposes a multi-frequency disturbance observer (DOB) to address this issue. In this paper, a periodic disturbance observer (PDOB) is employed to suppress periodic disturbances. Based on this, a series of multi-resonance terms are introduced to enhance the performance of the Q filter in PDOB to suppress certain aperiodic current harmonics. The effectiveness of the proposed method in suppressing harmonics is validated through simulations, showcasing its superiority over PDOB. This method not only presents a viable solution to the stator current harmonic in dual three-phase motors but also offers versatility for application in other systems necessitating harmonic mitigation.