Hilbert-Huang transform is a new time-frequency technology of processing non-stationary signal based on empirical mode decomposition, which can get the instantaneous time-frequency property for different intrinsic mode functions. Compared with conventional time-frequency technique, Hilbert-Huang transform has its advantage in resolving and stationary of signal, and can realizes the linear instantaneous time-frequency analysis of seismic signal with physical significance, and describes the relationships among time, frequency and energy of seismic signal more delicately, by which, the sedimentary cycles of different levels can be classified. The analysis results of model data and actual seismic data show that the time-frequency analysis of seismic data processed by Hilbert-Huang transform can accurately classify different level stratigraphy sedimentary cycles. And that, it is a simple process with high precision, which provides a new feasible method and reference for sedimentary cycles classification and fine stratigraphy correlation.