Content-based histopathological image retrieval (CBHIR) has become popular in recent years in the domain of histopathological image analysis. CBHIR systems provide auxiliary diagnosis information for pathologists by searching for and returning regions that are contently similar to the region of interest (ROI) from a pre-established database. While, it is challenging and yet significant in clinical applications to retrieve diagnostically relevant regions from a database that consists of histopathological whole slide images (WSIs) for a query ROI. In this paper, we propose a novel framework for regions retrieval from WSI-database based on hierarchical graph convolutional networks (GCNs) and Hash technique. Compared to the present CBHIR framework, the structural information of WSI is preserved through graph embedding of GCNs, which makes the retrieval framework more sensitive to regions that are similar in tissue distribution. Moreover, benefited from the hierarchical GCN structures, the proposed framework has good scalability for both the size and shape variation of ROIs. It allows the pathologist defining query regions using free curves according to the appearance of tissue. Thirdly, the retrieval is achieved based on Hash technique, which ensures the framework is efficient and thereby adequate for practical large-scale WSI-database. The proposed method was validated on two public datasets for histopathological WSI analysis and compared to the state-of-the-art methods. The proposed method achieved mean average precision above 0.857 on the ACDC-LungHP dataset and above 0.864 on the Camelyon16 dataset in the irregular region retrieval tasks, which are superior to the state-of-the-art methods. The average retrieval time from a database within 120 WSIs is 0.802 ms.