For the influence of residual unbalance and sensor error on the microvibration control accuracy of the magnetically suspended rotor system, a high-precision harmonic vibration force suppression method using a finite-dimensional adaptive filter is proposed. The double-input finite-dimensional adaptive filter is constructed by using the orthogonal characteristic of the output signals of the rotor radial X and Y displacement sensors. On the basis of harmonic current suppression, the power amplifier is taken as a controlled object, and a displacement stiffness force feedforward compensation loop is constructed. The influence of the low-pass characteristic of the power amplifier is fully considered, and the error-free tracking characteristic of the adaptive filter is used to make the deviation of the synchronous input signal zero, and then the high-precision compensation of the synchronous displacement stiffness force is realized. In addition, by changing the gain factors of different subfilters, the suppression effect at each harmonic frequency can be guaranteed, and finally, the microvibration control of the magnetically suspended rotor system can be further realized. The feasibility and effectiveness of this method are verified by experimental research.