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Based on the Hilbert–Huang spectral analysis, a method is proposed to identify multi‐degree‐of‐freedom (MDOF) linear systems using measured free vibration time histories. For MDOF systems, the normal modes have been assumed to exist. In this method, the measured response data, which are polluted by noises, are first decomposed into modal responses using the empirical mode decomposition (EMD) approach with intermittency criteria. Then, the Hilbert transform is applied to each modal response to obtain the instantaneous amplitude and phase angle time histories. A linear least‐square fit procedure is proposed to identify the natural frequency and damping ratio from the instantaneous amplitude and phase angle for each modal response. Based on a single measurement of the free vibration time history at one appropriate location, natural frequencies and damping ratios can be identified. When the …