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Currently, studies of archaeological stratigraphy strongly rely on spatial pattern. In this paper, we propose an approach for building the 3D model of archaeological stratigraphy, and introduce a method that combines spatial data statistics with spatial pattern recognition of archaeological stratigraphy. The 3D model is based on the IDL language programming, and the integrated 3D visualization system is based on the Micorsoft.NET platform development. In the integrated 3D visualization system, we can analyze the spatial distribution trend of stratigraphic units, reconstruct the original appearance of excavation units, and deduce the sedimentary processes. As a case study, we apply the modeling technique to Jinsha Site. Results indicated that the excavation pits can be shown in an active 3D scene and spatial characteristics can be identified with quantitative descriptions.