The deep subspace clustering method, which adopts deep neural networks to learn a representation matrix for subspace clustering, has shown good performance. However, this representation matrix ignores the structural constraint when it is applied to subspace clustering. It is known that samples from different classes can be taken as embedding in independent subspaces. Thus, the representation matrix should have a block diagonal structure. This paper presents the Deep Subspace Clustering with Block Diagonal Constraint (DSC-BDC), a model which constrains the representation matrix with block diagonal structure and gives a block diagonal regularizer for learning a suitable representation. Furthermore, to enhance the representation capacity, DSC-BDC reforms the block-diagonal structure constraint by performing a separation strategy on the representation matrix. Specifically, the separation strategy ensures that the most compact samples are selected to the represent data. An alternative optimization algorithm is designed for our model. Extensive experiments on four public and real-world databases demonstrate the effectiveness and superiority of our proposed model.