Pilots' brain fatigue status recognition faces two important issues. They are how to extract brain cognitive features and how to identify these fatigue characteristics. In this article, a gamma deep belief network is proposed to extract multilayer deep representations of high-dimensional cognitive data. The Dirichlet distributed connection weight vector is upsampled layer by layer in each iteration, and then the hidden units of the gamma distribution are downsampled. An effective upper and lower Gibbs sampler is formed to realize the automatic reasoning of the network structure. In order to extract the 3-D instantaneous time-frequency distribution spectrum of electroencephalogram (EEG) signals and avoid signal modal aliasing, this article also proposes a smoothed pseudo affine Wigner-Ville distribution method. Finally, experimental results show that our model achieves satisfactory results in terms of both recognition accuracy and stability.