Near infrared spectroscopy (NIRS) analysis technology, combined with chemometrics, can be effectively used in quick and nondestructive analysis of quality and category. In this paper, an effective drug identification method by using deep belief network (DBN) with dropout mecha-nism (dropout-DBN) to model NIRS is introduced, in which dropout is employed to overcome the overfitting problem coming from the small sample. This paper tests proposed method under datasets of different sizes with the example of near infrared diffuse reflectance spectroscopy of erythromycin ethylsuccinate drugs and other drugs, aluminum and nonaluminum packaged. Meanwhile, it gives experiments to compare the proposed method's performance with back propagation (BP) neural network, support vector machines (SVMs) and sparse denoising auto-encoder (SDAE). The results show that for both binary classification and multi-classification, dropout mechanism can improve the classification accuracy, and dropout-DBN can achieve best classification accuracy in almost all cases. SDAE is similar to dropout-DBN in the aspects of classification accuracy and algorithm stability, which are higher than that of BP neural network and SVM methods. In terms of training time, dropout-DBN model is superior to SDAE model, but inferior to BP neural network and SVM methods. Therefore, dropout-DBN can be used as a modeling tool with effective binary and multi-class classification performance on a spectrum sample set of small size.