In this paper, a three-dimensional model for the dynamic analysis of a flywheel based on the finite element method is presented. The static structure analysis for the model provides stress and strain distribution cloud charts. The modal analysis provides the basis of dynamic analysis due to its ability to obtain the natural frequencies and the vibration–made vectors of the first 10 orders. The results show the main faults are attrition and cracks, while also indicating the locations and patterns of faults. The harmonic response simulation was performed to gain the vibration response of the flywheel under operation. In this paper, we present a Hilbert–Huang transform (HHT) algorithm for flywheel vibration analysis. The simulation indicated that the proposed flywheel vibration signal analysis method performs well, which means that the method can lay the foundation for the detection and diagnosis in a reactor main coolant pump.