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 novel structural damage identification method based on transmissibility in the time domain is proposed. The method takes the discrepancy of transmissibility of structure response in the time domain before and after damage as the basis of finite element model updating. The damage is located and quantified through iteration by minimizing the difference between the measurements at gauge locations and the reconstruction response extrapolated by the finite element model. Taking advantage of the response reconstruction method based on empirical mode decomposition, damage information can be obtained in the absence of prior knowledge on excitation. Moreover, this method directly collects time-domain data for identification without modal identification and frequent time–frequency conversion, which can greatly improve efficiency on the premise of ensuring accuracy. A numerical example is used to demonstrate the overall damage identification method, and the study of measurement noise shows that the method has strong robustness. Finally, the present work investigates the method through a simply supported overhanging beam. The experiments collect the vibration strain signals of the beam via resistance strain gauges. The comparison between identification results and theoretical values shows the effectiveness and accuracy of the method.