A scheme is suggested to identify instantaneous frequencies and instantaneous damping ratios of time-varying dynamic system by applying empirical mode decomposition and Hilbert transform to the system responses. Applicability of the identification algorithm is first numerically validated through a 2 -story frame structure model. Then, the method is adopted to analyze the responses of a 12-story shear wall structure model, which is tested on a shaking table, to identify its instantaneous dynamic properties. The identified instantaneous damping ratio is introduced into the finite element model to compute the structural responses, and is further compared with those obtained by constant damping ratio and measurement. The comparison reveals that responses using the instantaneous damping ratio are much closer to the test results.