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Non-stationary EEG noise from simultaneous fMRI-EEG acquisition could be conventionally removed by optimal basis selection and followed by a low-pass filtering. An empirical model decomposition (EMD) method was applied to partially remove non-stationary EEG noise from simultaneous fMRI-EEG acquisition. Our results suggested that EMD method could reveal similar auditory evoked potential with optimal basis selection and low-pass filtering without prior knowledge or cut-off frequency, thus preserving high frequency signal not empirically related to the non-stationary noise. This EMD method allows us to investigate human brain high frequency EEG oscillation in the simultaneous fMRI-EEG measurement.