Abstract: Hybrid stepper motor (HSM) has extremely small internal damping, which often leads to excessive oscillation and even lost steps during actual operation. To improve the control quality of stepper motor, a stepper motor active damping control method based on IHF-PLL³rd is proposed. First, the active damping control utilizes a synchronous d-q coordinate system to adjust the stator current, which controls the i_d constant to the rated current, and adjusts the i_q to generate instantaneous torque to suppress oscillation. Secondly, a third-order phase locked loop (PLL³rd) combined with an integral harmonic filter (IHF) is proposed for speed observation aiming to implement a closed speed loop to increase motor damping. The PLL³rd can avoid the steady-state error during the acceleration and deceleration of the motor, while IHF can effectively filter out the higher harmonic components in the back electromotive force. This method solves the problem that only the oscillation magnitude is reduced, while the damping of the control system remains unchanged in the traditional micro-stepping control. Finally, the proposed scheme is experimentally verified to be effective.