The present invention discloses a brain activity analysis method and apparatus, which is based on a nonlinear waveform decomposition technology, wherein the changes of the intrinsic features in brain waves are decomposed and demodulated to extract the modulation signals of the components, including the frequency-modulation signals and the amplitude-modulation signals. The present invention further uses a feature mask to determine whether to proceed further decomposition and demodulation of the extracted modulation signals. If not, the multidimensional changes of the intrinsic features are obtained according to the feature mask. Then, quantitation and identification is performed to obtain the status of brain function. The present invention not only effectively increases the accuracy of the identification but also uses the feature mask to obviously reduce the complexity and the load of computation.