When performing a modal analysis of a structural system with close modes or high damping, the results of identification may be poor due to modal interference, which refers to the phenomenon that vibration energy of each mode of a system may overlap with other modes within certain frequency range, the estimation of system order is thus important to the effectiveness of modal identification. In this paper, by introducing the concept of the singular value decomposition (SVD) in Ibrahim Time-Domain method (ITD), and the order of system matrix is efficiently determined, and the modal identification of a system with close modes through the ITD method can then be well implemented. Numerical simulation of one example of a model of the railway vehicle, confirm the validity of the proposed method for system identification of a structure with modal interference.