Structural damage identification technology is of great significance to improve the reliability and safety of civil structures and has attracted much attention in the study of structural health monitoring. In this paper, a novelty structural damage identification method based on the transmissibility in time domain is proposed. The method takes the discrepancy of transmissibility of structure response in time domain before and after damage as the basis of finite element model modification. The damage location and damage degree are obtained through iteration by minimizing the difference between the measurements at gauge locations and the reconstruction response extrapolated by FE model. Taking the advantage of the response reconstruction method based on empirical mode decomposition, the damage information is possible to obtain in the absence of prior knowledge on external excitation information. Moreover, this method is carried out in the time domain, without the need to identify the modal parameters and perform time-frequency analysis, which simplicity ensures the high efficiency of damage identification. The effectiveness and accuracy of the proposed method are studied by simulation, including reconstruction error and measurement noise. The identification results demonstrate that the proposed structural damage identification method improves the calculation effectiveness considerably and ensures the identification accuracy.