A kind of modified model method based on FRF is presented in this paper. By the method, the damage identification for the structure of IASC-ASCE SHM Benchmark is conducted. The result reveals that the error of model analysis and the influence of measurement noise on the modification can be reduced significantly, and the physical meaning of matrix can be ensured to be clear and definite during modifying. Under the effect of model error, measurement noise and the uncertainty of mass and stiffness, the method displays good accuracy of identification.