This study has two major concentrations: 1) exploring methods of creating a digital city model, and 2) applying the model to study urban spatial structure, an issue of particular interest and importance to urban planners. Based on existing studies that primarily address two-dimensional (2D) urban structure, this paper focuses on the three-dimensional (3D) structure relating to the 3D urban form. Given their greater clarity and possibilities for quantitative analysis, both 3D digital urban models and GIS spatial overlay analysis methods hold tremendous potential for analysing and predicting future urban form. In this project, the Xidan Business District in Beijing’s Inner City was the area selected to implement the digital-city application. Under the hypothesis that the existing urban spatial structure is determined by the city’s urban planning scheme and current urban marketing forces, it is found that actual urban development does not follow the planning restrictions on zoning and building height regulations. Some contradictions and conflicts, such as building location and height, appeared in the studied district. The specific reasons for the discrepancies need to be further studied.