Dynamic analysis method of anisotropic asymmetric rotor-bearing system based on 3D finite element method was presented. The system mass, stiffness and coriolis force matrices expressed in the rotating coordinate system were generated by ANSYS. Time-varying bearing stiffness in the rotating coordinate was then obtained by coordinate transform. The differential equations of motion of the system were generated by applying constraints and time-varying bearing stiffness to the system matrices using the corresponding relationship between node number and column index of the matrices. Floquet theory and Hill infinite determinant method were adopted to solve the differential equations and frequency characteristics and stability of the system were obtained. The proposed method was validated based on a literature model, and the proposed method was applied to the dynamic analysis of an industrial rotor considering the anisotropic asymmetric characters.