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This paper put forward a method which is based on Fast Fourier Transform (FFT) and Hilbert Huang transform (HHT) to improve the accuracy of modal parameters identification. Firstly, FFT was used to determine the approximate range of each natural frequency, and then filter the signal by the bandwidth filter in order to reduce the effects of noise and each other mode to the empirical mode decomposition (EMD), and ensure the accuracy of the EMD method. Secondly, freedom response of single mode is extracted by using the EMD method based on the correlation coefficient to decompose the denoised signal. Finally, the natural frequency and damping ratio are identified after finishing the freedom response's Hilbert spectral analysis (HSA). The results of modal parameters identification on actual measured signal of the circuit board indicate that the identified natural frequencies and damping ratio by the proposed method are closer to the true results.