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This paper proposes an effective method for over-voltage classification based on the Hilbert-Huang transform（HHT） method.Hilbert-Huang transform method is composed of empirical mode decomposition（EMD） and Hilbert transform.Nine kinds of common power system over-voltages are calculated and analyzed by HHT.Based on the instantaneous amplitude spectrum,Hilbert marginal spectrum and Hilbert time-frequency spectrum,three kinds of over-voltage characteristic quantities are obtained.A hierarchical classification system is built based on HHT and support vector machine（SVM）.This classification system is tested by 106 field over-voltage signals,and the average classification rate is 94.3%.This research shows that HHT is an effective time-frequency analysis algorithms in the application of over-voltage classification and identification.