A shaft control method and device for a magnetic suspension system. The shaft control method for the magnetic suspension system includes: acquiring a displacement signal obtained by detecting displacement of a shaft in the magnetic suspension system (Step 101); separating whirling displacement from the displacement signal (Step 102); and controlling whirling of the shaft according to the whirling displacement (Step 103). By the disclosure, the effect of suppressing the whirling of the shaft during high-speed rotation of the magnetic suspension system is achieved.