Three-dimensional (3D) geological modeling is an interdisciplinary research as well as a research hotspot. In this paper, a 3D stratum automatic modeling method based on Voronoi diagram of borehole planar point set is proposed in solving the problems of low modeling efficiency, low automation degree and lack of identification of stratum pinch and interlayers in current modeling method. The method firstly analyzes and processes the borehole data and classifies them according to the attributes of the stratigraphic blocks. Then the stratigraphical boundary is identified based on the Voronoi diagram through the determination of plane connectivity and elevation connectivity. Finally, the stratigraphic blocks are divided into two types, ordinary stratum and interlayer stratum respectively, with geologic model built for different strata. The method has been applied to an underground project of Nanjing, showing that it’s suitable for the modeling of sedimentary strata and in a better position to identify the pinch and interlayer phenomena commonly seen in the strata distribution, realizing the rapid and automatic modeling without human intervention.