Abstract: To enhance the reliability of power systems for electric vertical takeoff and landing aircraft and logistics drones in low-altitude economic applications, the fault-tolerant control of dual three-phase permanent magnet synchronous motors under open-phase fault conditions is investigated. In the fault-tolerant control strategy based on an invariant decoupling matrix, voltage transfer errors in the faulty phase introduce second-harmonic currents and torque ripple. Although the direct voltage compensation method avoids the conflict between the current controllers of the fundamental plane and the harmonic plane, it is essentially a harmonic open-loop control, which has problems such as parameter sensitivity, noise amplification, and instability. To address these challenges, an closed-loop online voltage error compensation strategy based on an extended state observer is proposed. In this method, an ESO is employed for closed-loop control in the harmonic plane to estimate and compensate for disturbances in real time, thereby effectively suppressing current harmonics and torque ripple under fault-tolerant operation while maintaining the system’s decoupled structure. The experimental results demonstrate that under a single-phase open-circuit fault, both the phase current waveform and torque ripple are significantly improved with the proposed fault-tolerant strategy, verifying its effectiveness.