In this paper, we propose a family of novel Deep Hierarchical Transitive-Aligned Graph Kernels (DHTAGK) for graph classification. To this end, we commence by developing a new Hierarchical Aligned Graph Auto-Encoder (HA-GAE) to construct transitive-aligned embedding graphs that encapsulate the structural correspondence information between graphs. The DHTAGK kernels then measure either the Jensen-Shannon Divergence between the adjacency matrices or the Gaussian kernel between the node feature matrices of the embedding graphs. Unlike the classical R-convolution kernels and node-based alignment kernels, the DHTAGK kernels can capture the transitive structural correspondence information and thus ensure the positive definiteness. Furthermore, the HA-GAE enables the DHTAGK kernels to simultaneously reflect both local and global graph structures and identify common structural patterns. Experimental results show that the DHTAGK kernels outperform state-of-the-art graph kernels and deep learning methods on benchmark datasets.