A credible large-scale three-dimensional (3D) geological model constructed from a small amount of local high-density data provides a vital data infrastructure for the design and construction of metro lines. The multiple-point statistics (MPS) method has successfully generated 3D geological models in many fields. However, the global cognition of the spatial relations between geological objects is difficult to reconstruct using a local optimization strategy with moving templates in the MPS simulation. This study presented an MPS simulation approach for constructing 3D geological structures with two-dimensional (2D) cross-sections, where the MPS process was coupled with a fully connected deep neural network (FCDNN) simulation. The core idea of the proposed method was that the global features of each geological object were generated from the trained FCDNN, the input parameter of which was the subsurface depth. Then, the entire model was constructed on the initial model using the following iterative MPS process: the semantic relationship of geological objects was extracted from 2D cross-sections and used as a constraint in the modeling process, which ensured the order of the stratigraphic sequence and rationality of the geological structure in the final model. The joint objective function of the proposed method was composed of the loss function of the FCDNN and conventional MPS objective function constrained by the spatial semantics of geological objects. The concrete example in the Jiangtai Road Metro Station of Guangzhou Line 11, China illustrated that the details of the complex geological structures could be obtained accurately by the presented method. The global features from the trained FCDNN provided the basic geometry for the final model, which overcame the limitations of the conventional MPS method.