Creating 3D geographical simulations have been useful to many applications of geological information. Generally, typical CG simulations cannot properly and accurately represent the multilayer geographical data, due to the lack of ability to display the relations or connections between each soil layer. Also, there are errors in the position of soil layers, and classification of soil layers which does not correspond to the actual data. This research therefore presents a 3D hydrogeological data which can display the complex internal structure of soil layer classification, and can calculate required geological information, such as the position of soil layers, the cross section of soil layers and height contours, accurately in correspondence to the actual data. Calculation to create the simulation begins by specifying the position of each soil layer, and then creating a surface for each soil layer by estimating from the received depth inputs, to calculate the cross section of each soil layer at critical heights calculated based on Morse theory. After that, we create the Reeb graph to create the surface and the complete internal structure of the geological information, which can be displayed in three-dimensions, with the ability to display soil layer cross sections and the soil layer structure, and it can also be used to represent and store the geographical information systematically for efficient retrieval.