In this study, advanced computational technique for mechatronic analysis has been developed for the efficient design and test of typical machine tool models. Flexible multi-body dynamic (FMBD) analysis method combined with motion controller including control logics is used to simulate typical operation conditions. The present FMBD machine tool model is composed of flexible column structure, rigid body spindle, vertical motion guide (arm) and screw elements. Driving motor clement with rotating degree-of-freedom is interconnected and governed by the designed Matlab Simulink control logic, and then the position of the spindle is feedback into the control logic. It is practically shown from the results that the investigation of designed machine tools with controller can be effectively conducted and verified.