The dynamic simulation of machine tools and motion control systems has been widely used for optimization, design verification, control design, etc. There are three main streams in dynamic simulation: structural dynamic analysis based onthe finite element method, dynamic motion analysis based on equations of motion, and control system analysis based on transfer functions. Generally, one of these dynamic simulation methods is chosen and employed for specific purposes. In this study, an integrated dynamic simulation is introduced, in which the structure, motion, and control dynamics are combined together. Commercially well-known software is used in the integrated dynamic simulation: ANSYS, ADAMS, and Matlab/Simulink. Using the integrated dynamic simulation, the dynamics of a magnetic bearing stage is analyzed and the causes of oscillation and noise are identified. A controller design for suppressing a flexible dynamic mode is carried out and verified through the integrated dynamic simulation.