The propulsion shafting and the main shaft of fluid machinery of ships and submarines supported by magnetic bearings may subjected to the axial external excitation force at work. When the force is transmitted to the base, it would cause the base vibration and seriously affect the working stability. Therefore, the use of the magnetic bearing to isolate the constant frequency external excitation force is of great significance. In order to solve the problem that the rotor may be disturbed by the external excitation force of constant frequency in the process of operation, the magnetic bearing control method based on notch filter can be used for vibration isolation. The introduction of the notch filter weakens the active control effect of the magnetic bearing on the external exciting force frequency of the rotor vibration, so that the exciting force of the rotor could be transmitted to the base as small as possible, so as to achieve the purpose of the base vibration reduction. Taking the magnetic bearing rotor test-bed as the research object, the simulation of external excitation and external excitation experiment of exciter were carried out. The analysis and comparison of axial vibration isolation, axial and radial vibration isolation were completed. The experimental results show that the vibration acceleration of the frame can be reduced by more than 95％when using the test-bed to simulate the external excitation force of the rotor, and by about 60％when using the vibration exciter to apply the excitation force to the rotor.