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Three-dimensional entity model is the base of visualization and application of true 3D GIS. Nowadays, digital terrain model of aboveground spatial data with various scales and resolutions is much more convenient in building digital city. However, it is difficult to build efficiently 3D body model based on huge amount of underground spatial data that is unstructured and very complicated. This paper gives an efficient and quick modeling method with three layers to deal with mass underground spatial data. The related key issues include: (1) 3D underground body model considering their geometrical, topological and semantic relationship. (2) Efficient underground spatial body index to support dynamic dispatch of 3D complicated magnanimity data. (3) Technology of genetic algorithm and expert system introduced to make the processing of building 3D geological entity model more intelligently and accord with geologists' idea. (4) Parallel modeling by divisions of cities according to geological rules and regulations. To utilization of cities' underground space, the 3D body modeling method for mass underground spatial data provides a new way for great amount of 3D geological data, 3D engineering data, and so much as true 3D GIS spatial data.