According to the purpose of applications, the application program will utilize the most suitable data model and 3D modeling data would be generated based on the selected data model. In these reasons, there are various data sets to represent the same geographical features. The duplicated data sets bring serious problems in system interoperability and data compatibility issues, as well in finance issues of geo-spatial information industries. In order to overcome the problems, this study proposes a spatial data fusion method using topological relationships among spatial objects in the feature classes, called Topological Relation Model (TRM). The TRM is a spatial data fusion method implemented in application-level, which means that the geometric data generated by two different data models are used directly without any data exchange or conversion processes in an application system to provide indoor LBSs. The topological relationships are defined and described by the basic concepts of IndoorGML. After describing the concepts of TRM, experimental implementations of the proposed data fusion method in 3D GIS are presented. In the final section, the limitations of this study and further research are summarized.