The understanding of geographical reality is a process of data representation and pattern discovery. Former studies mainly adopted continuous-field models to represent spatial variables and to investigate the underlying spatial continuity/heterogeneity in the regular spatial domain. In this article, we introduce a more generalized model based on graph convolutional neural networks (GCNs) that can capture the complex parameters of spatial patterns underlying graph-structured spatial data, which generally contain both Euclidean spatial information and non-Euclidean feature information. A trainable semi-supervised prediction framework is proposed to model the spatial distribution patterns of intra-urban points of interest(POI) check-ins. This work demonstrates the feasibility of GCNs in complex geographic decision problems and provides a promising tool to analyze irregular spatial data.