Villages areas hold significant importance in the study of human-land relationships. However, with the advancement of urbanization, the gradual disappearance of spatial characteristics and the homogenization of landscapes have emerged as prominent issues. Existing studies primarily adopt a single-disciplinary perspective to analyze villages spatial morphology and its influencing factors, relying heavily on qualitative analysis methods. These efforts are often constrained by the lack of digital infrastructure and insufficient data. To address the current research limitations, this paper proposes a Hierarchical Graph Neural Network (HGNN) model that integrates multi-source data to conduct an in-depth analysis of villages spatial morphology. The framework includes two types of nodes-input nodes and communication nodes-and two types of edges-static input edges and dynamic communication edges. By combining Graph Convolutional Networks (GCN) and Graph Attention Networks (GAT), the proposed model efficiently integrates multimodal features under a two-stage feature update mechanism. Additionally, based on existing principles for classifying villages spatial morphology, the paper introduces a relational pooling mechanism and implements a joint training strategy across 17 subtypes. Experimental results demonstrate that this method achieves significant performance improvements over existing approaches in multimodal fusion and classification tasks. Additionally, the proposed joint optimization of all sub-types lifts mean accuracy/F1 from 0.71/0.83 (independent models) to 0.82/0.90, driven by a 6% gain for parcel tasks. Our method provides scientific evidence for exploring villages spatial patterns and generative logic.