To analyze a multibody system composed of non-uniform beam and spring-mass subsystems, the model discretization is carried on by utilizing the finite element method(FEM), the dynamic model of non-uniform beam is developed by using the transfer matrix method of multibody system(MS-TMM), the transfer matrix of non-u- niform beam is derived, and the natural frequencies are computed. Compared with the numerical assembly method (NAM), the results by MS-TMM have good agreement with the results by FEM, and are better than the results by NAM. When using the high precision method, the global dynamic equations of the complex multibody system are not needed and the orders of involved system matrices are decreased greatly. For the investigation on the re- verse problem of the physical parameter identification of multibody system, MS-TMM and the optimization tech- nology based on genetic algorithms(GAs) are combined and extended. The identification problem is exchanged for an optimization problem, and it is formulated as a global minimum solution of the objective function with respect to natural frequencies of multibody system. At last, the numerical example of non-uniform beam with attach- ments is discussed, and the identification results indicate the feasibility and the effectivity of the proposed aop- proach.