Numerous problems are encountered in human-computer interaction modeling. This modeling only qualitatively considers the impact of stratum loss and demonstrates its high cost and long cycle. Moreover, human-computer interaction modeling fails to update the model and quickly build high-precision models in a large area. Automatic modeling disregards the influence of stratum loss. Therefore, the interpolation is still conducted in the area with no target layer, which expands the distribution range of the target layer and causes low model accuracy. First, the discrete thin plate spline function method was used in this paper for interpolation based on the current automatic modeling technology. Then, the stratum thickness DEM was accurately and reasonably generated to determine the formation boundary and analyze the stratum form quantitatively. Finally, a complex 3D geological model for the main urban area of Guangzhou City (1 500 km²) was automatically constructed. The actual drilling proves the reasonability and accuracy of the model. The proposed modeling method can markedly improve the efficiency of large-area modeling and reduce the modeling time and cost, which is conducive to the rapid update of the model.