Especially in the EMS (Electronics Manufacturing Service) companies which manufacture IT product components, reduce the production cost by applying high speed tracking motions capability from machine tools. Therefore higher speed tracking motion always required. However, the motion accuracy gets worse due to mechanical vibration by means of the inertia in high speed motion, the speed is limited. The vibration due to the interaction of feed drive systems with the machine tool structure has a great influence on the relative position between tool and workpiece. In order to improve motion accuracy, the model that can analyse the influence is required. The purpose of this study is to develop a mathematical model which can investigate the relative motions between tool and workpiece. In order to achieve the purpose, in this study, a state space equation model of an NC machine tool which considers vibration of machine tool structure is proposed based on analysed vibration mode of the machine. This model also considers the torsion vibration of the bed and motion characteristics of the feed drive systems. The mass, inertia, stiffness and viscosity are determined based on the calculation and identification by matching the frequency responses. In order to evaluate the effectiveness of the proposed model, vibration modes are simulated and compared with the measured ones. In addition, corner tracking motions and circular motions are measured and simulated. Motion trajectories of feedback position (rotational angle of motors), linear scale positions (axial displacements of the table), and relative position between the spindle nose and the table are measured and simulated in the motions. As the results, it is confirmed that the proposed model can predict the vibration mode and the motion trajectories.