Traditional spatio-temporal data model based on relational database, which will result in hard to convert problem domain model to relational model, complicated query and low expansibility. In view of this, we propose the spatio-temporal data model (STDM) based on graph database. The data model integrated TGIS’s three key elements: space, time and attributes, expressed spatio-temporal characteristics of TGIS explicitly. Finally, the paper gave a particular description of logistics distribution route optimization. Experimental results show that the model is proved to be good for expressing the spatio-temporal process.