A geological model that integrates the surface and subsurface is significant for exploring and developing coal seam gas resources. It is the basis for selecting favourable areas of the coal seam gas field, locating coal seam gas wells, and their drilling design. GIS software is powerful in three-dimensional (3D) geographical modeling but weak in 3D geological modeling. To realize the integration of geographical and geological models in GIS software, expanding its 3D geological modeling ability is necessary. In this paper, a 3D geological modeling scheme was integrated into ArcGIS software products. After decomposing and reorganizing the 3D geological modeling workflow using object-oriented methods, a new method for automated geological modeling based on ArcGIS Engine components is proposed, and its key algorithms were designed, such as accurate positioning and high-resolution representation of geological bodies. Finally, using ArcGIS Engine components and Visual Studio C# as the software development platform, the 3D geosciences modeling software system was developed and implemented. The result is an effective way to quickly achieve the integrated modeling of 3D surface and subsurface data based on the GIS software system.