Due to the difficulty in identifying parameters of the large and complex structure, a damage identification method combining model updating based on the frequency response function (FRF) method with the substructure method was proposed. An optimization equation about the FRF after damage was constructed. Then, the damage parameters were identified by updating the substructure finite element model (FEM) to FRF after damage. A three-layer plane frame was used as a numerical example. The calculation results show that the algorithm is more sensitive to damage parameters and has higher recognition accuracy. The method can accurately identify the predefined substructure damage elements and degree.