Aiming at the problem that the unbalanced vibration of a high-speed magnetically suspended rotor affects the attitude angular velocity measurement accuracy of magnetically suspended control and sensitive gyroscope (MSCSG), a multifrequency vibration suppression method based on adaptive multifrequency estimation (AMFE) is proposed. First, the reason of rotor mass unbalance vibration is analyzed, the dynamic model of MSCSG with unbalance vibration is established, and its influence on spacecraft attitude angular velocity measurement accuracy is pointed out. The multifrequency vibration suppression controller and the compensation module of residual synchronous displacement stiffness force are designed when the rotor speed is unknown. The measurement signal of the radial <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${X}$ </tex-math></inline-formula> -channel displacement sensor and its orthogonal signal are used to realize the estimation of the rotor speed. Finally, the convergence of the AMFE algorithm and the stability of the system are analyzed. The simulation and experimental results show that the proposed method can effectively suppress harmonic currents and residual synchronous displacement stiffness disturbance force caused by mass imbalance. The method proposed in this article can effectively improve the attitude angular velocity measurement accuracy of MSCSG.