The End Point Selection Method which solves the end effect of EMD (Empirical Mode Decomposition) is proposed. It adds a judging and selecting procedure to find the most suitable points which can fit the perfect envelopes in each sifting process. And an improved EMD-based structural damage feature extraction is proposed. Then, the improved EMD-based structural damage feature extraction is applied to an aircraft composite wing-box. The damage feature index-relative variation of instantaneous frequency is extracted. The damage feature index is more with the increasing structural damage degree.