CNC machine tools has always screw joints in its feed drive systems; In order to obtain good performance of CNC machine tool, it is necessary to model the screw joint with more accuracy and to research its influence on the vibration characters of the feed drive system. In this paper, the screw joint is analyzed by multi-body system theory and is modeled as flexible multi-body; Its mathematical describe of constraint condition is given by the modeling of screw joint. A revise factor is introduced into the process of FEM simulation to reflect the deformation in the screw joint. By this way, the effect of deformation in the screw joint is researched in the modeling under the ANSYS circumstance, the harmonic response under considering deformation contrast to that of without deformation. From the analysis in the simulation, it is necessary to take the deformation of screw joint into account.