Abstract: A new method is proposed to analyze the nonlinear and non-stationary signals based upon the technique of empirical mode decomposition (EMD). Analysis program of nonlinear signals is developed on the basis of this method, which it can separate the vibration signals into multiple eigenfunctions. Comparing EMD method with traditional FFT method in the analytical process, HilbertHuang transformation is found to be superior in performance. Structural response of the warship subjected to underwater explosion is simulated numerically, and EMD method is applied to analyzing the structural impulse signals. The components and characteristics of the acceleration signals of underwater explosion impulse are analyzed essentially by researching each of the eigenfunctions. It can be instructive for the analysis of underwater explosion impulse signals.