For large-area foundation treatment sites with uneven spatial distribution of soft soil layers and large thickness differences，3D geological model has been built and contour map of the soft soil thickness has been drawn by Civil 3D，which is a more intuitive way to display the distributions of the soft soils. According to the settlement calculation results of typical borehole with different soft soil thickness，and giving consideration to both treatment effect and construction cost，three different foundation treatment schemes have been adopted for the soft soils of different thickness：no plug-in board and no piling，plug-in board without piling，plug-in board and piling.In addition，the software Civil 3D is used to calculate the quantities of surcharge preloading material and realize the refinement of the ground treatment process through 3D modeling，which can effectively overcome the shortcomings of large computation and insufficient calculation accuracy of the method of section. It is a reference for the fine design of foundation treatment for the land-forming project of the automated container stack yard.