The rotor mass imbalance is common in rotating machinery, which can lead to the synchronous vibration in the magnetically suspended centrifugal compressor (MSCC) system. This work proposes a synchronous vibration control method based on the optimal notch filter. Firstly, the dynamics of the magnetically suspended rotor (MSR) system with mass imbalance is modeled. Then phase-shift notch filter for the synchronous vibration suppression is designed according to theoretical stability analysis of the whole system. Furthermore, in order to optimize the dynamic performance of the notch filter, its phase angle is taken as the variable to be optimized. Taking the integral of the absolute value of time multiplies current as the objective function, the optimized design flow of the phase angle is given. The proposed optimized method does not rely on accurate mathematical model, and is more direct. Finally, the simulation and experiment results demonstrate the effectiveness of the optimal notch filter and also prove the system stability.