Abstract: Hilbert-Huang transform (HHT) is a novel data analysis method which can be used to process nonlinear, non-stationary data and is very adaptive. A 45-storey RC frame structure and its shake table test model were briefly introduced. The structural response records under different seismic intensities were analyzed with HHT method, and the time-frequency-amplitude and Hilbert marginal spectrum were obtained. The result shows that Hilbert spectrum can clearly present the energy distribution with time and frequency. Most energy of Hilbert spectrum is much more concentrated in the definite range of time and frequency. The Hilbert spectrum can grasp main characteristics of the signal. Hilbert marginal spectrum curve and natural vibration frequency at peak amplitude vary with different seismic intensity. The same trend of all figures shows that Hilbert marginal spectrum can be used in the safety assessment of civil engineering structures.