Empirical mode decomposition(EMD) method has been recently proposed to analyze non-linear and non-stationary data. This method allows the decomposition of one-dimensional signals into intrinsic mode functions(IMFs) and is used to calculate a meaningful multi-component instantaneous frequency. In this paper, it is assumed that each mode of damped vibration signal could be well separated in the form of IMF by EMD. In this case, we can have a new powerful method to calculate natural frequencies and dampings from damped vibration signal which usually has multiple modes. This proposed method has been verified by both simulation and experiment. The results by EMD method whichhas used only output vibration data are almost identical to the results by FRF method which has used both input and output data, thereby proving usefulness and accuracy of the proposed method.