To predict the dynamic characteristics of seeker servo mechanism in the process of precision assembly, the quantitative relationship between the micro assembly parameters and the resonance frequency of servo mechanism was built by using the theoretical modeling method. Based on the Hertz contact theory, a five-degree-of-freedom bearing stiffness model was established and the influence of the micro assembly errors on the bearing stiffness matrix was modeled and analyzed. Using the theory of Timoshenko beam, the cell matrix of elastic multi-diameter shaft was derived. The method of solving the eigenvalue and eigenvector of the whole system was determined. An analysis system for resonant frequency of servo mechanism was established through using MATLAB/GUI and the experimental system was established to verify the theoretical model. The analysis and experimental results show that the established analytical method and system can accurately calculate the resonant frequency variation caused by the microassembly errors of bearing. This method solves the problem of dynamic characteristic prediction in the process of precision assembly of servo mechanism.