This paper presents a multi-body flexible dynamic analysis of a centrifugal turbo blower for a fuel cell electric vehicle (FCEV) based on the application of computer-aided engineering (CAE) to predict the acceleration at the mount position of the blower. This predicted acceleration is validated by using the measured acceleration data. The numerical simulation for the multi-body flexible dynamics of the blower is used not only to identify the most effective mount among four mounts in an FCEV by controlling the complex stiffness of the isolator, but also to suggest the range of complex stiffness of the isolator at the most effective mount. This numerical simulation technology can be useful for the estimation of the variation of vibration transmission for the structural modification of the turbo blower.