The three-dimensional (3D) geological model is one of the end-product of geological information generated as a result of analysis based on the fundamental field data and the knowledge/interpretation of the geologist. In Japan Society of Geoinformatics, many research papers related to the construction of 3D geological model have been reported since the formation of the Japanese Society for Geological Data Processing (the predecessor of this society) in 1979. In this paper, the 3D geological model construction/visualization and the geological boundary surface estimation have mainly been described, which have been mainly discussed in the Japan Society of Geoinformatics. The results of these researches were presented and updated with improvements and enhancements keeping pace with the evolution of computers over the years since inception of the Japanese Society for Geological Data Processing. The basic mathematical principle for the model construction was formulated by around 2000. In the following decade, development of algorithms as standalone packages and integration into general-purpose GIS for 3D geological modeling were completed. Subsequently, the research and development focused on promoting practical use and wider dissemination. Over the period of time, more robust algorithms for estimation of geological boundary surface has also been advanced. Presently, several of the research outcomes have provided technical basis for commercial 3D geological modeling software that have been developed and used in practical business. Finally, the current status and future prospect of the 3D geological modeling is described from the viewpoints of model creators and users.