The inverse sub-structuring method can predict the component-level frequency response functions (FRFs) of product (critical component) for product transport system from only measured system-level FRFs, facilitating the cushioning packaging design. However, the FRFs of the coupling interface between product and vehicle are usually of extreme difficulty to be measured due to the limited accessible space. To overcome this difficulty, the authors suggested a so-called FRF probe technique method in the previous study, which may be more suitable for the single-coordinate coupled system. In practice, most of the product transport systems should be treated as multi-coordinate coupled system. The aim of this paper is to derive a new FRF-based inverse sub-structuring method for multi-coordinate rigidly coupled product transport system and develop a new shearing probe technique to obtain the difficult-to-monitor FRFs at the coupling interface, which will be validated by a lumped mass model and finite element models, respectively, showing perfect agreement. Finally, the experiment on a physical prototype of multi-coordinate rigidly coupled product transport system is performed to further check the feasibility of the application prospect of the shearing probe technique for inverse analysis of product transport system. The method proposed in this study will provide the packaging designers an alternative method to monitor the integrity of product transport system.