Due to the influence by the noise mixed into the vibration responses of flood discharge structure, the analysis precision of vibration responses will be reduced. According to the characteristics of IMFs decomposed from white noise, the calculation method of noise standard deviation in each IMF is studied, and the filtering method based on EMD and Wavelet-threshold is improved. Aimed at the difficult problem of exciting the prototype to test, combined with the characteristic of ambient excitation, a method based on NExT and HHT is utilized to identify the modal parameters. Finally, the method mentioned in this paper is applied to the dynamic test and vibration responses analysis of Ertan arch dam and Yingxiuwan hydropower station sluice respectively. The results show that this method has good applicability in vibration responses analysis of flood discharge structure.