Abstract: In order to solve the problem of health monitoring at local area of large bridges, a double-element substructure method to identify the physical parameters of bridge structures is proposed. This method is a finite element-based time domain system identification approach, in which the physical parameters of only two adjacent elements can be identified each time. In the paper, a bridge structure is divided into finite elements. The state and observation equations are established for arbitrary two adjacent elements. Using the extended Kalman filter, the physical parameters including stiffness, mass and damping of the substructure are obtained. Taking a 3-span continuous beam bridge as an example for simulation, the physical parameters of the substructure of the bridge are identified under different noise levels. The results show that the parameters can be identified correctly and efficiently, which proves the effectiveness of the proposed method.