Abstract: Electric tractors have been widely used in agricultural production in recent years, Among them, the decoupling structure can be adopted as an electric power-take-off (PTO) system, due to its flexible control. A variable leakage flux permanent magnet (VLF-PM) Motor can be expected to serve as the driving motor for the PTO system, in order to improve the efficiency of electric tractors. Light load wide speed regulation and high torque for heavy loads can fully meet the needs of different working conditions. However, the complex disturbances have often limited the VLF-PM motor drive system under the PTO system of electric tractors. Particularly, motor parameters, load shocks, and system failures can seriously disturb the operational accuracy and efficiency of the PTO system. In this article, a compensation control strategy was proposed for the complex disturbance of the VLF-PM motor drive system under electric tractor PTO. Firstly, the control performance of the motor was varied significantly, according to the VLF-PM motor electromagnetic parameters and uncertain external disturbances, such as load shocks, soil conditions, and different crops. A sliding mode anti-disturbance control strategy was designed using a nonlinear disturbance observer (NDO). Specifically, a separate design was adopted in the sliding mode to greatly reduce the complexity of parameter adjustment for the dynamic and steady-state performance of the motor. In the control system of NDO, the strong anti-disturbance performance was required to resist the impact of the fault. The reason was that there was the a greater and more fatal impact of PTO motor failure on click work efficiency. The lumped disturbances after faults were compensated to suppress the impact of perturbing system faults for the robustness of the motor. A quasi-resonant feedforward nonlinear disturbance observer was designed for the stability of VLF-PM motor speed and torque output under faults. A series of experiments were carried out to validate the control strategy at different PTO standard speeds. A load test was firstly conducted on the VLF-PM motor, in order to verify its feasibility of PTO motor. The results demonstrated that the motor was maintained a typical standard speed output during loading, indicating the higher efficiency, compared with the traditional interior permanent magnet synchronous motors. Secondly, the performance of three control methods—PID, traditional ADRC, and SMC-NDO was compared under parameter and load disturbances. The results showed that the SMC-NDO was reduced the speed oscillation and adjustment time by 60.0% and 13.4%, respectively, indicating the most effective anti-interference performance. Therefore, the high operational accuracy was fully met the requirements of electric tractors; The frequency of the fault disturbance signal was consistent with theoretical analysis during current sensor faults and motor phase loss. The disturbance observation level was returned to the normal state. Meanwhile, the q-axis feedback current ripple was suppressed under improved observer control. Once the current sensor failed, the output torque ripple decreased by 33.6%, 69.0%, and 49.7%, respectively, under three operating conditions. The output torque ripple decreased by 68.5%, 51.4%, and 52.8%, respectively, under phase loss fault. At the same time, there was almost no pulsation in the speed, when the motor failed. This control strategy was effectively improved the anti-disturbance and system robustness of the PTO motor. The findings can provide new ideas and references on the anti- disturbance and efficient operation of electric tractors.