With the popularity of application of BIM technology, the related BIM authoring tools are becoming more powerful to support the IFC standard, and scale and semantic details of IFC models are becoming more complicated. Then, how to store IFC model efficiently to promote the model application is a challenge in the research area. This paper applies the method of knowledge base to describe how to store IFC data model and IFC case file in the graph database. A metadata knowledge base and a case knowledge base are both established, and the dependency of the two above knowledge base models is analyzed. In an actual commercial complex model, the time efficiency and space efficiency of knowledge base storage are verified. Based on the establishment of knowledge base, this paper further analyzes the case of using the Cypher language to query the IFC knowledge base, which effectively solves the problems related to IFC version comparison, entity relationship sorting and spatial relationship mining. The study provides an important reference for the combination of knowledge base and the AEC industry.