The paper aims to propose an indirectly inverse sub-structuring method for multi-substructure system to solve the problems that the inverse sub-structuring method for rigidly can't be applied when system-level coupling interface FRFs are difficult to be measured. Based on the sub-structuring theory, an indirectly inverse sub-structuring method for multi-substructure system was proposed firstly. Then a corresponding lumped parameter model was established to obtain the directly calculated component-level FRF and predicted ones by known parameters and formulas. Finally, the results were compared. The predicted FRFs showed great agreement with directly calculated ones, which verified accuracy of the method. The proposed method can provide a new way for the inverse sub-structuring theory to solve the problem of the difficult-to-monitor coupling interface FRFs. It provides more possibilities in the wider application of the transportation packaging field.