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The Hilbert-Huang transform (HHT) is a new analysis method suitable for nonlinear and non-stationary signals. It is very appropriate to seismic signals because they show both non-stationary and nonlinear characteristics. We first introduce the realization of HHT empirical mode decomposition (EMD) and then comparatively analyze three instantaneous frequency algorithms based on intrinsic mode functions (IMF) resulting from EMD, of which one uses the average instantaneous frequency of two sample intervals having higher resolution which can determine that the signal frequency components change with time. The method is used with 3-D poststack migrated seismic data of marine carbonate strata in southern China to effectively extract the three instantaneous attributes. The instantaneous phase attributes of the second intrinsic mode functions (IMF2) better describe the reef facies of the platform margin and the IMF2 instantaneous frequency attribute has better zoning.Combining analysis of the three IMF2 instantaneous seismic attributes and drilling data can identify the distribution of sedimentary facies well.