As near-infrared spectroscopy has many advantages, such as fast analysis, non-destructive testing and field detection, it has been widely used in many fields. However, there are some shortcomings such as low signal-to-noise ratio, weak absorption intensity and overlapping peaks in near-infrared spectroscopy. NIR spectroscopy can not be qualitatively/quantitatively obtained from the spectrum. Therefore, NIR spectroscopy can only be used as an indirect analytical technique. The research of infrared spectral modeling method becomes the core of analyzing near infrared spectroscopy. Deep learning is a new branch of machine learning and has been successfully applied in many fields. The network structure of deep learning and the non-linear activation ability make the model especially suitable for high-dimensional and nonlinear large-scale data modeling. In order to further enrich the NIRS modeling method and improve the accuracy of NIRS, it is necessary to develop a new modeling method using NIRS. The qualitative analysis of near-infrared spectroscopy is studied in this paper. A model based on Stacked Contractive Auto-Encoders(SCAE) is proposed to identify the same drugs produced by different manufacturers on the market. With contractive Auto-Encoder (CAE) based on Auto-Encoder network by adding Jacobi matrix as a constraint, self-coding network is used to reduce the dimension of the data to learn the internal characteristics of the data, and Jacobi matrix contains information in all directions. The extracted features can be invariant to a certain degree of perturbation of the input data and improve the ability of self-encoding network to extract features. SCAE is a multi-layer CAE neural network. As the input layer of the latter layer of CAE network, all the parameters of the network are obtained by adopting the layer-by-layer greedy training method. After the training, all the networks are regarded as a whole, Fine-tuning by backpropagation algorithm, and finally using Logistic/Softmax classifier for qualitative analysis. The experimental data were collected by the National Institutes for Food and Drug Control, with Cefixime Capsules as the second classification experimental data and Isosorbide Dinitrate Tablets as a multi-classification experimental data. The spectral curves were obtained by measuring the absorbance of each sample at different wavelengths with a Bruker Matix spectrometer, and then the deviation from the spectral samples was obtained by OPUS software to eliminate the drift and other factors. Next, we established the model by experimentally determining the Lamda of the constrained Jacobi matrix ratio coefficient of 0.003. The modeling process was divided into five stages, namely: pre-treatment stage, pre-training stage, fine-tuning stage, testing stage and contrast stage. In order to verify the performance of SCAE network in terms of classification accuracy, algorithm stability and modeling time, the algorithm was compared with BP neural network, SVM algorithm, sparse Auto-Encoders (SAE), Denoising Auto-Encoders(DAE) for comparison. In terms of classification accuracy, stack compression self-coding network has the highest classification accuracy and algorithm stability at different ratios of training set to test set. In terms of modeling time, SVM algorithm has a great advantage over other algorithms in terms of running time because it does not need pre-training and feature extraction. However, stack compression self-coding network modeling speed is better than other contrast algorithms except SVM. In summary, the use of stack compression self-coding network for drug identification is effective and feasible.