A finite element model was built up based on the 3-D model of the large and high effective milling machine of CNC.The finite element analysis software-ANSYS was applied to the modal analysis of the machine tool.The preceding nine step natural vibration frequencies and its corresponding vibration modes were obtained.The deficiency of the machine tool was pointed out.Four different kinds of models were established towards the deficiency and their calculations were solved.A reasonable scheme was provided through the comparison.