The motor rotation assembly of machine tools is mainly composed of spindle, rotor and bearings, it is to some extent the most important component, and its dynamic characteristics directly affect the machining accuracy and efficiency. Although the finite element method is effective to solve such dynamic problem, the conventional method generally ignores the influence of assembly tolerance between the spindle and the rotor .This probably would lead to a larger error result. A new method is described to evaluate the results obtained from finite element analysis .Firstly, a finite element mathematical model of motor rotation assembly is established, and then the model is tested by means of modal experiment, finally, the mathematical model results calculated by MATLAB software is compared with that of modal experiment, the results show that this modeling method is accurate and efficient. Furthermore, rotors of different inner diameters are mounted onto the spindle of same size, and then modal experiment and a finite element analysis are applied to obtain the dynamic characteristics of the motor rotation assembly under different assembly tolerances. This research can provide some reference values for the tolerance design of the motor rotation assembly.