The three-dimensional (3D) geological structure model has been the basic preconditions for the analysis of urban underground space, because it can directly display the spatial distribution and geological properties of superficial deposits and provide basic data for the scientific planning of the underground space resources. In this paper, the authors constructed for the very first time a 3D geological structure model (up to the depth of 50m from the surface) in Beijing City, based on almost a thousand boreholes, investigation reports, as well as 107 intersecting cross-sections arranged over Beijing City within the 5th Ring Road. The authors investigated the 3D modeling procedures in the study area, where an extremely complicated sedimentary environment is developed with various geological phenomena including intersecting stratigraphic interfaces, missing strata as well as discontinuous layers. The resulting 3D model could provide a basic framework and data support for further geological evaluation of underground space resources.