The purpose of superconducting magnetic bearing flywheel energy storage system(SMB-FESS) is to store unused nighttime electricity as kinetic energy and convert it to electricity during daytime. The SMB-FESS is proposed as an efficient energy storage system because there is no mechanical problems, such as friction and wear The flywheel over SMB is rotated at a high speed, 50,000rpm. The major source of energy loss in the SMB-FESS is vibration of flywheel. Therefore, the vibration characteristics of SMB-FESS should be identified. In this study, the axial/radial stiffness and damping coefficient of SMB are measured by a vibration test. Natural frequencies and natural modes of flywheel and magnet are analyzed by a finite element method. The modal analysis of system is performed using the modal parameters of each component and the measured stiffness/damping coefficient. So, natural at frequencies and mode shapes of the joined system can be obtained. According to critical speed analysis, the system has two rigid conical modes in the low speed range. Nevertheless, the system has not been affected by the critical speed in the main operating range.