The article focused on the three-level rigid-flexible coupling packaging system. The system-level FRFs were used to predict the component-level FRFs, and the formula for inverse substructure analysis was deduced. Based on the characteristics of rigid and flexible coupling systems, the three-level rigid-flexible coupling system was transformed to two-level rigid and flexible coupling systems respectively, and results were obtained by theoretical derivation and verified with the lumped parameter model to perform error analysis of the theoretical formula. The correctness of the theoretical formula was verified and based on this theory, the influencing pattern of each measuring transfer function on predicted FRFs was obtained. The study provided theoretical reference for dynamic mechanical analysis of the rigid-flexible coupling packaging system.