GIS modelling, which is often employed to establish the abstract structural forms of geological phenomena and their structural relationships, is of great importance for the expression and analysis of geological structures to describe and express such phenomena accurately and intuitively. However, current GIS modelling schemes value structural forms over structural relationships, and existing geological semantic expressions in the modelling of geological relationships are incomplete. Therefore, this paper categorizes geological relationships into three levels: geological phenomena, geological objects and geological spatial objects: (1) based on their definitions, this work categorizes geological relationships into internal composition relationships and external combined relationships for a total of two categories, eight classes and 27 small groups; (2) this work also improves the system with a total of 33 classified geological objects by transforming the relationships between geological phenomena into relationships between geological objects; and (3) based on the 27 small groups of geological relationships, through the corresponding geometric and semantic expressions between topological rules and geological rules and between relationship rules and geological rules, this work then expresses internal composition relationships as topological relationships between geological spatial objects and expresses external combined relationships as association relationships between geological spatial objects. A GIS model of geological relationships that integrates their geometries and semantics is then built. Finally, taking the Dagang-Danyang section of the Ningzhen mountains as an example, the results show that the proposed GIS modelling method can better store and express geological phenomena, geological objects and geological spatial objects in a way that integrates geometry and semantics.