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In the field of ship-borne PMSM, there exists the sea wave fluctuations, external disturbances thus model uncertainties are always challenging the control design of ship-borne permanent magnet synchronous motors (PMSMs). To deal with this problem, a super-twisting extended state observer (SESO) is used in this paper to observe state variables accurately. Moreover, to solve the phase delay problem in active disturbance rejection control (ADRC), Taylor’s formula-based tracking differentiator (TTD) is applied in the proposed hybrid control strategy. With appropriate compensate of disturbance, denoted as super-twisting hybrid control, the controlled position signal can follow the reference with small tracking errors, also with improved dynamic performance. Simulation results show that the proposed super-twisting hybrid control has the better anti-disturbance and tracking performance compared with the traditional ADRC. Lastly, semi-physical experimental results further validate the effectiveness of the control strategy for ship-borne PMSMs.