A relative displacement between cutter and workpiece formed by Incremental linear superposition, which is created by all joints of the whole structure system of high-speed NC milling machine, influences the machining precision. In this study, connection relations of major components in machine tool are analyzed. The corresponding minimum displacement of vibration mode between the principal axis and workpiece in low order mode of the whole machine is adopted as the evaluation indicator of dynamic performance advantages and disadvantages. The comprehensive analysis is conducted on natural frequency and vibration mode of machine tool through the assembly of modal force matrix, so as to search out the corresponding maximum modal frequency and weak structural links, to correct modal frequencies of main structural components for separation, to avoid substantial increase of the whole vibration amplitude caused by the fact that the driving frequency of the whole machine is close to the modal frequency of component and to achieve the goal of optimizing the whole structure. Compared with the whole finite element, the analytical accuracy error of this method is less than 2.5% and the analysis time can be reduced by 50%.