In recent years, the necessity of the incorporation of semantic information into three-dimensional city models (3DCMs) has become a consensus in 3D GIS field. In order to provide practical support for visual applications concerned with semantics, this paper firstly presents an extended semantic model based on the CityGML standard, which was worked out for the general storage and representation of semantics. In this model, concepts like Room, Corridor and Stair are all derived from concept Space which corresponds to the concept of Room in CityGML. This extension will benefit the indoor structure representation. Geological feature is also supported by the model for the underground analysis. Next, for the promotion of semantic modeling by this model, a semi-automatic process of semantic enrichment is implemented in a data integration tool. It provides an adaptive way to link semantics with pure geometry. Finally, two typical cases of visual exploration are illustrated to prove the model's practicability in a national 3D GIS project of China. One is indoor routing, which adopts this model to extract the geometric path and thus enrich traditional semantic-enhanced navigation routine; another case is unified profiler, where semantics are intergrated in order to fill up the cross section correctly and ensure the topological and semantic consistency.