A method for synchronously inhibiting subcritical vibrations of magnetic levitation molecular pump rotor, by use of synchronously sampling signals of subcritical vibrations of the rotor generated after the rotor of the magnetic levitation molecular pump touches down so as to obtain the amplitude and the phase of subcritical vibrations of the rotor, based on which a compensation force is output for inhibiting subcritical vibrations of the rotor. Through using the present method, an accurate synchronous for signals of subcritical vibrations and fast inhibition for subcritical vibrations of the rotor is achieved.