Industry Foundation Classes (IFC) files are commonly used for data exchange of Building Information Models (BIMs). Due to the equivalent transformations in the graph structure of IFC data, it is a challenge to perform version comparison and incremental storage on IFC files. In this paper, an IFC normalization method is proposed, which can reduce the influence of the equivalent transformations, so that the normalized IFC file can be directly used in Git-like tools for version comparison and incremental storage. The algorithm is also designed for getting stable results when running on multi-threads. Experiments show the efficiency of the algorithm and its potential in Common Data Environment (CDE) applications.