The invention discloses a substructure response reconstruction method and system, and a storage medium. The method employs model condensation to generate a super-unit model based on a finite element model, does not need to consider the boundary conditions of all substructures, can better adapt to the dynamic response reconstruction of a large-scale complex engineering structure, and expands a current time domain reconstruction method based on EMD decomposition, the modal synthesis is used in the response reconstruction method for the first time, the response of each main modal in the whole substructure is reconstructed based on the interface response of the known substructure, the response reconstruction only needs to be carried out under the condensed substructure, and then the main modeof a super-unit model is expanded to the response of the degrees of freedom of all internal units in the finite element model through coordinate back calculation, so that the accuracy is ensured, thereconstruction efficiency is greatly improved, the computer memory is saved, and the analysis speed is high.