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It is difficult to analyze high resolution sequence stratigraphy accurately and scientifically. This paper develops a new method of multi-level stratigraphy sedimentary cycles classification based on seismic data. Seismic signal processed by Hilbert-Huang transform can be decomposed into basic mode components of different resolution. The instantaneous time-frequency characteristics of these mode components can describe the relationship among time, frequency and energy accurately, and their mirror-image contrast can classify different level sedimentary cycles. The analysis results of model data and actual seismic data show that time-frequency analysis of seismic data processed by Hilbert-Huang transform can accurately classify different level stratigraphy sedimentary cycles.