The invention discloses a magnetic suspension bearing control system capable of realizing resuspension after destabilization. Ball bearings are respectively mounted at the positions of two ends of a rotor. Elastic supporting seats sleeve the ball bearings. Protection clearances between slideable supporting seats and the outer rings of the ball bearings can be eliminated after magnetic suspension bearing destabilization. High-frequency vibration possibly generated after the rotor falls is converted into low-frequency vibration in the direction of supporting springs so as to introduce an electromagnetic damping force. If the magnetic suspension bearing control system operates normally according to the judgment, a rotor position control module in a controller is adopted for the magnetic suspension bearing control system; if the magnetic suspension bearing control system operates abnormally according to the judgment, the controller controls the elastic supporting seats to operate, in this like, original high-frequency large-amplitude vibration state is changed into low-frequency larger-amplitude vibration in the direction of the supporting springs; a damping force control module is adopted for controlling the magnetic suspension bearing control system, so that the electromagnetic damping force is applied to the rotor to reduce the vibration amplitude of the rotor; and at last, the damping force control module is converted into the rotor position control module so as to realize resuspension.