A method and a system for processing an electroencephalogram (EEG) signal are provided. The method for processing the EEG signal includes: performing a spike detection on the EEG signal to obtain a spike distribution waveform, performing an instantaneous frequency oscillation energy analysis on the EEG signal to obtain multiple energy distribution waveforms; performing a complexity analysis on the EEG signal to obtain a complexity change waveform, obtaining a determination result of a specified neural waveform based on the spike distribution waveform, the energy distribution waveforms, and the complexity change waveform, and outputting the determination result.