An optimized method for whole machine tool dynamic characteristics based on machine structure energy distribution is proposed after the finite element model (FEM) of a vertical machining center has been accurately established. The spring-damping system is adopted to establish the FEM with ANSYS to simulate the contact behaviors of its joint surface based on the identified joint stiffness and damping. Then, the modal characteristics and harmonic responses of the whole machine are analyzed. The FEM is verified to be accurate and the weak modes are obtained after comparing its results with that of the experiments. The elastic energy of the whole machine tool and the joints of these weak modes are calculated. The joints with a relatively high ratio of whole machine tool elastic energy are regarded as the weak joints. Finally, an optimized project based on the stiffness of these weak joints is proposed. The results show that the elastic energy ratio of each weak joint of the weak modes and the dynamic response amplitudes of the spindle tip decreases. Thus, the feasibility of this optimized method is verified with the improvement in the dynamic characteristics of the whole machine tool.