In order to realize the stable and precision control of elastic beams in large overall rotation at high speed, its nonlinear dynamic model must be built and the decoupling work should be completed. Flexible rod was assumed by Euler-Bernoulli beam. The approach of assumed modes was applied to discrete the coordinates, and the Galerkin method and Hamilton principle were adopted to establish the flexible dynamic model. The regular perturbation formula was deduced with perturbation theory. Multiscale method was used to improve the perturbation formula by separating two-time parameters. The decoupling accuracy was deeply analyzed for the regular perturbation method and the improved perturbation method.The validity and feasibility of the proposed method were verified by Runge-Kutta method. The simulation data indicated that the improved perturbation solution owned high decoupling accuracy, little computation and good rapidity. The problem of low decoupling accuracy was solved compared with the common regular perturbation method which was limited by effective time series. The proposed decoupling method also avoided much calculation caused by high-order perturbation to improve the computation’s accuracy. It provided an important theoretical basis and data support for dynamic decoupling about complex multi-body flexible systems.