An accurate identification of the flutter derivatives of bridge deck section model in wind tunnel requires the information of dynamic properties of the bridge, including natural frequencies and damping ratios. This paper presents a method of identifying natural frequencies and damping ratios of the bridge deck section of different wind velocity. Firstly, we adopt the EMD technique to decompose the response signal of the model vibration into several mono-component signals which become analytic signal by means of Hilbert transform. Then each mono-component signal is analyzed via wavelet transform to identify the frequency and damping ratio. The results demonstrate that the combination method of EMD and Morlet wavelet transform can be used to identify the frequency and damping ratios effectively. The numerical simulation and the analysis of the response signal data from the bridge deck sectional model show that this method is effective.