For large and complex structures with repetitive characteristics, a multi-stage substructure dynamic analysis method based on modal synthesis is proposed to effectively improve the efficiency of simulation calculation. First, the repetitive components are taken as the primary substructure, and the components that produce local modes in the primary substructure are taken as the secondary substructure. The modal synthesis method is used to truncate all modal characteristics of the secondary substructure, and the constrained modal parameters and main modal parameters of the primary substructure are obtained. Then, according to the spatial coordinates, the primary substructure stiffness matrix and mass matrix are repeatedly assembled to obtain the condensation model of the whole structure. The condensation model is used for dynamic simulation to obtain the acceleration load of the substructure installation interface. Finally, the internal dynamic response of the substructure at all levels is obtained by using the super-element method. The simulation analysis of space-borne phased array synthetic aperture radar antenna shows that the multi-stage substructure dynamic simulation analysis results are highly consistent with the traditional analysis results, and the calculation efficiency is increased by more than four times. The substructure dynamic analysis method is reasonable and reliable.