We present a novel hierarchical modeling method for layout representation learning, the core of design documents (e.g., user interface, poster, template). Existing works on layout representation often ignore element hierarchies, which is an important facet of layouts, and mainly rely on the spatial bounding boxes for feature extraction. This paper proposes a Spatial-Structural Hierarchical Auto-Encoder (SSHAE) that learns hierarchical representation by treating a hierarchically annotated layout as a tree format. On the one side, we model SSH-AE from both spatial (semantic views) and structural (organization and relationships) perspectives, which are two complementary aspects to represent a layout. On the other side, the semantic/geometric properties are associated at multiple resolutions/granularities, naturally handling complex layouts. Our learned representations are used for effective layout search from both spatial and structural similarity perspectives. We also newly involve the tree-edit distance (TED) as an evaluation metric to construct a comprehensive evaluation protocol for layout similarity assessment, which benefits a systematic and customized layout search. We further present a new dataset of POSTER layouts which we believe will be useful for future layout research. We show that our proposed SSH-AE outperforms the existing methods achieving state-of-the-art performance on two benchmark datasets.