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One issue of GIS is management of huge amount of spatial data. Nowadays, acquisition capacity of 3D spatial data with various scales and resolutions is much more convenient due to new 3D acquisition technologies. It is a difficulty that how to efficiently and synthetically organize and manage large scale underground 3D spatial data with contents of continuous distribution and nonuniformity. A 3D GIS data management system framework with three layers is proposed to deal with large scale underground data integrated management. The related key issues and methods include: (1) Multi-scale underground spatial object concept model. (2) 3D spatial database model considering spatial and semantic relationship and corresponding data structure is introduced to support extendable storage environment such as file system, typical commercial database management system and cluster parallel system. (3) True 3D spatial index considering level of detail (LOD). (4) Efficient dynamic dispatch method of great amount of 3D spatial data is adopted based on 3D data content and associated information. (5) 3D spatial data engine (SDE) provides a uniform access interface for file management system, relational database management system and cluster parallel system and other applications. The 3D GIS database model focuses on the key issues of massive underground 3D spatial data provides a new way for the high performance database organization and management of true 3D geological data as well as its integration with the aboveground spatial data.