A 3D city model is the digital representation of the terrain and objects in an urban area in which buildings can be modeled in different LOD levels. According to the entity-based concept of GIS, an entity is defined as an independent existent object type in the real world which is composed of spatial features and attributes. Following this concept, if the 3D building models are introduced to a GIS environment for query process and data analysis, the attributes should be reorganized corresponding to the spatial data. This paper investigates the changes of a GIS environment in the aspects of visualization, query process, and data analysis when the 3D city model is introduced. In the future, the entity-based 3D city model will be developed which is not only for visualization, but also can be used for query process and data analysis as a GIS.