Exploiting graph-structured data has many real applications in domains including natural language semantics, programming language processing, and malware analysis. A variety of methods has been developed to deal with such data. However, learning graphs of large-scale, varying shapes and sizes is a big challenge for any method. In this paper, we propose a multi-view multi-layer convolutional neural network on labeled directed graphs (DGCNN), in which convolutional filters are designed flexibly to adapt to dynamic structures of local regions inside graphs. The advantages of DGCNN are that we do not need to align vertices between graphs, and that DGCNN can process large-scale dynamic graphs with hundred thousands of nodes. To verify the effectiveness of DGCNN, we conducted experiments on two tasks: malware analysis and software defect prediction. The results show that DGCNN outperforms the baselines, including several deep neural networks.