This paper provides the methodology on analyzing the dynamic characteristic of machine tool in consideration of joint parameters. To ensure the dynamic model is available for further study, modal experiment for vertical machining center is involved. The machine tool is divided into several parts and connected with spring and damping for substructure modeling. Particularly, the bolt-fixed joint is an example for the joints modeling. Based on the dynamic model, simulation of modal analysis and harmonic response are carried out. Besides, method of optimization design of column and milling box is given to improve the performance, which is proved to be feasible in harmonic response.