High order active vibration suppression technology has been gradually applied to the multi-order vibration of space infrared mechanical cryocooler to improve the working life of cryocooler and the working performance of infrared load. When the mechanical cryocooler is driven by high-order working frequency, it will produce serious harmonic distortion, which will affect the active suppression effect of high-order vibration. By analyzing the working mechanism of the driving circuit and the high-frequency characteristics of the load, the method of using the control freewheeling path to suppress the harmonic distortion in high-order driving is put forward, and the corresponding implementation method according to the required freewheeling path is also presented. For one of the freewheeling methods, simulation and experiments show that the scheme can effectively suppress the waveform distortion and reduce the high-order harmonic distortion by more than 75%.