Abstract: Aiming at the low optimization efficiency of the large structural damage identification in civil engineering, a Substructure Virtual Distortion Method (SVDM) is presented base on Virtual Distortion Method (VDM). VDM is a fast structural reanalysis method which uses virtual distortions to simulate structural damages, and the modified structural responses can be estimated quickly without rebuilding the whole structural finite element model. Based on the VDM, the way of virtual distortions of the substructure is reduced to simulate its damages through the eigen-decomposition of the substructure stiffness matrix and the analysis of the structural motion equation, and thus it extends the application of the VDM to more complex practical structures. Via analysing the correlations of the distortions with structural responses, the main virtual distortions of the substructure are picked up to reflect the damages. The correlation estimation equation is presented. This reduces the number of necessarily-considered virtual distortions and increases the computational efficiency. A numerical 50-story frame model is used to verify the proposed method.