3D model retrieval has been widely utilized in numerous domains, such as computer-aided design, digital entertainment and virtual reality. Recently, many graph-based methods have been proposed to address this task by using multiple views of 3D models. However, these methods are always constrained by the many-to-many graph matching for similarity measure between pair-wise models. In this paper, we propose an hierarchical graph structure learning method (HGS) for 3D model retrieval. The proposed method can decompose the complicated multi-view graph-based similarity measure into multiple single-view graph-based similarity measures. In the bottom hierarchy, we present the method for single-view graph generation and further propose the novel method for similarity measure in single-view graph by leveraging both node-wise context and model-wise context. In the top hierarchy, we fuse the similarities in single-view graphs with respect to different viewpoints to get the multi-view similarity between pair-wise models. In this way, the proposed method can avoid the difficulty in definition and computation in the traditional high-order graph. Moreover, this method is unsupervised and is independent of large-scale 3D dataset for model learning. We conduct extensive evaluation on three popular and challenging datasets. The comparison demonstrates the superiority and effectiveness of the proposed method comparing with the state of the arts. Especially, this unsupervised method can achieve competing performance against the most recent supervised & deep learning method.