A hierarchical recognition system (HRS) based on constrained Deep Belief Network (DBN) is proposed for SAR Automatic Target Recognition (SAR ATR). As a classical Deep Learning method, DBN has shown great performance on data reconstruction, big data mining, and classification. However, few works have been carried out to solve small data problems (like SAR ATR) by Deep Learning method. In HRS, the deep structure and pattern classifier are combined to solve small data classification problems. After building the DBN with multiple Restricted Boltzmann Machines (RBMs), hierarchical features can be obtained, and then they are fed to classifier directly. To obtain more natural sparse feature representation, the Constrained RBM (CRBM) is proposed with solving a generalized optimization problem. Three RBM variants,L1-RNM,L2-RBM, andL1/2-RBM, are presented and introduced to HRS in this paper. The experiments on MSTAR public dataset show that the performance of the proposed HRS with CRBM outperforms current pattern recognition methods in SAR ATR, like PCA + SVM, LDA + SVM, and NMF + SVM.