The goal of this research is to develop a design and optimization methodology for the mechatronic modules of machine tools by treating all important characteristics from all involved engineering domains in one single process. In this study, a mechatronic system of machine tools was broken into a structure and control two-level systems. In the first stage for structure design process, the Pro/E was used to build up the 3D models and the AnSys was employed to design the mechanical structure and select the optimal components for the machine tools. Next, in the control design process, a common controller type was designed by MATLAB in this stage. Then, three important parameters were established for the machine tools design to achieve the overall system performance.