An unbalance identification and vibration suppression control system for a magnetic suspension rotating machinery comprises an unbalance identification module, an unbalanced force compensation module, a magnetic bearing power amplifier, an electromagnet rotor and a displacement sensor. Based on stable control of a magnetic suspension rotor, the unbalance of a magnetic bearing is identified in an online manner by a novel wave trap based on coordinate transformation, on one hand, the identification amount is used for compensating common-frequency current stiffness force, on the other hand, proper common-frequency current stiffness force is generated according to the identification amount to compensate common-frequency displacement stiffness force, and the influence of the low-pass characteristic of the power amplifier on compensation precision of the common-frequency displacement stiffness force is eliminated by leading a simplified inverse model of the magnetic bearing power amplifier into a feed-forward channel. When the magnetic suspension rotor rotates at a high speed, common-frequency bearing force is greatly reduced, and unbalanced vibration of the magnetic suspension rotor is remarkably suppressed. The unbalance identification and vibration suppression control system is simple, convenient, easy and particularly suitable for an actual high-speed magnetic suspension rotor system.