The work aims to optimize the traditional inverse sub-structuring method, to get the dynamic response characteristic of sub-structure in nonlinear multi-coordinate coupled system, which is helpful to resolve the issue that complex coupling forms and nonlinear characteristic of material make it difficult to measure the physical parameters in transport packaging system. The description function method is used to linearize the nonlinear system and the frequency response functions (FRFs) at several response amplitudes need to be measured. Then, the modal parameters of the sub-structure can be identified by inverse sub-structuring method. Lastly, the relationship between the modal parameters and vibration amplitudes is fitted and a function is constructed to describe the dynamic response characteristic of the sub-structure. In the lumped parameter model, the predicted response was consistent with the actual. In the finite element model, the prediction error of the response peak was less than 5%, and the prediction error of the jumping frequency was less than 3%. The application of traditional inverse sub-structuring method was extended to nonlinear multi-coordinate coupled system, which had guiding significance for the construction of dynamic model of complex transport packaging system and the design of anti-vibration packaging.