In order to research the ways of establishing holistic finite element model based on properties of joints, the vibration modal of a vertical machining center KVC1050N is analyzed using the software ANSYS and the equivalences principle of fixed, rolling and sliding joints are introduced, which are compared with the modal testing. The result shows that the FE analysis vibration modal based on characteristics of joints accords with the test modal well, and the error of natural frequency for coherent vibration modes is about 15%, depending on which it analyses how stiffness of major joints effects holistic dynamic characteristics using the theory of orthogonal test, and these provide a new method for analysis and optimal design of the vertical machining center.