Thin-walled structures are commonly used in the design of mechanical systems, and their flexible dynamic problems are the frontiers in engineering research. In this paper, a flexible multibody system modeling method based on the shell theory is firstly developed for the dynamics of ammunition manipulator with thin-walled structure. We obtained the kinematic equation of the Reissner-Mindlin shell structure based on the floating frame of reference formulation. The coupling of membrane deformation and bending deformation with rigid motion is integrated in the proposed model, which is the characteristic of Reissner-Mindlin shell different from solid structure. In order to overcome membrane-locking and shear-locking problems in shell element simulation, an edge-center based strain smoothing - discrete shear gap (ECSS-DSG) element is introduced. The ECSS-DSG method achieves better membrane and bending behavior, as well as effectively overcoming shear-locking. Accordingly, the ECSS-DSG shows better performance in the structural analysis. Based on these works, the parameters of the ammunition manipulator model are identified by combining with experimental results. Subsequently, the prediction of model dynamic response under various working conditions is verified, which shows its excellent robustness. Our research can not only provide theoretical support for the further study of the ammunition manipulator, but also provide reference for the study of the dynamics of multibody system with thin wall structure.