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Improvements in hyperspectral image technology, diversification methods, and cost reductions have increased the convenience of hyperspectral data acquisitions. However, because of their multiband and multiredundant characteristics, hyperspectral data processing is still complex. Two feature extraction algorithms, the autoencoder (AE) and restricted Boltzmann machine (RBM), were used to optimize the classification model parameters. The optimal classification model was obtained by comparing a stacked autoencoder (SAE) and a deep belief network (DBN). Finally, the SAE was further optimized by adding sparse representation constraints and GPU parallel computation to improve classification accuracy and speed. The research results show that the SAE enhanced by deep learning is superior to the traditional feature extraction algorithm. The optimal classification model based on deep learning, namely, the stacked sparse autoencoder, achieved 93.41% and 94.92% classification accuracy using two experimental datasets. The use of parallel computing increased the model’s training speed by more than seven times, solving the model’s lengthy training time limitation.