Based on the principle of axial active magnetic bearing rotor-system with single degree of freedom, magnetic rotor-system vibration mode was described. A 3D finite element model of active magnetic bearing rotor-system was established by ANSYS11. Initial six order natural frequencies and vibration mode were calculated by the module of modal analysis of ANSYS11, and compared with the results of system identification. Analysis shows that there was a certain difference between the results, but the difference was small. The analysis result indicates that it is an effective method to apply FEA in the design of the active magnetic bearing. It provided the foundation for structure optimal design of the system and theoretical basis for flexible system design.