The invention relates to an active control method for minimal displacement of a magnetic suspension molecular pump rotor. A mathematical model of a generalized controlled object of a magnetic suspension rotor system is established by analyzing a formation mechanism of unbalanced vibration of the magnetic suspension rotor system. Channel controllers are designed based on the principle of linear auto disturbance rejection control. The unbalanced vibration of the system is regarded as an external disturbance, the disturbance is estimated and compensated in real time by using a linear extended state observer, and so same frequency compensation signals with appropriate amplitude and phase are superimposed on a control signal to offset rotor unbalanced exciting force to realize high speed and high precision rotation of the rotor around a geometric axis, thereby realizing the active control of the minimal displacement of the magnetic suspension rotor system. Compared with a conventional control method, the active control method has advantages of simple parameter adjustment, easy implement, small rotor whirl radius and high rotation precision, can greatly reduce rotation speed same frequency components in a displacement signal, and is of great significance for improving the performance and reliability of the magnetic suspension rotor system.