A structural geological model describes the structure of subsurface and plays an important role in the exploration of mineral and petroleum resources. Despite the widespread use of three-dimensional geological models, the theoretical research of informatics in the field of structural geology is still very limited. We have noticed a lack of methods for integrating explicit semantics of field observation data and geophysical data into geological models. The existing model representation methods focus on accurately representing the geometric morphological information of underground structures, ignoring the high-level semantics implied in the model. The formal representation of the semantic information is necessary to promote the development of intelligent methods in geomodeling and geophysical inversion. In this paper, we propose a new framework to formally represent the semantics of structural geological models with a clear distinction of geometric and geological semantics. For the geometric semantics, based on the extension of the 9-intersection model, we mathematically define the spatial topological relations between geometric objects that make up the geological model. For the geological semantics, we define the geological contact and compositional relations between geological bodies and geological surfaces and reveal the temporal implications of these geological relationships. We design a multilayer heterogeneous network as a computer characterization of the semantics of the geological model. A better representation of semantic information aids in the creation and validation of geological models, as well as management, queries, and analyses of geological knowledge.