The inverse sub-structuring method has been recently proposed and applied for inverse analysis of product transport system, to predict the component-level frequency response functions (FRFs) and the coupling dynamic stiffness from only the system-level FRFs. However, previous applications of this method were all developed based on the assumption that the components were coupled by flexible couplings. Actually, increasing more components are welded or bolted to construct a coupled system, which should be treated as rigidly coupled system. The aim of this paper is to derive a new FRF-based inverse sub-structuring method for the analysis of the dynamic characteristics of a two-component coupled product transport system with rigid couplings. And then a so-called FRF testing probe technique is proposed and applied to measure the difficult-to-monitor FRFs at the coupling interface. The developed method is verified by a lumped-mass model, showing exact agreement. Finally, the experiment on a physical prototype of two-substructure coupled product transport system is performed to further check the accuracy of the suggested method. The proposed method is an extension of previous inverse sub-structuring method and may help to obtain the main controlling factors and contributions from the various structure-borne paths for product transport system.