A new identification method for a nonproportional damping matrix using the finite element (FE) model updating technique is proposed. Mass and stiffness matrices of the undamped system are identified by FE model updating method. Sensitivity analysis is used to update the FE model, and zero frequencies are considered as design parameters to supplement the information of vibration characteristics. The nonproportional damping matrix is identified through the proposed method. A numerical example is considered to verify the performance of the proposed method. As a result, the damping matrix of the nonproportional system is estimated accurately.