Three-dimensional modeling of cities in the real-world is an essential task for city planning and decision-making. And many three-dimensional city models are being developed with the development of wireless Internet and location-based services that identify the location of users and provide the information increases for consumers. Especially, in case of urban areas of Korea, indoor space modeling as well as outdoor is needed due to the high-rise buildings densities. Also location-based services should be provided through spatial analysis such as the shortest path based on a space model. Many studies of three-dimensional city models are feature models. In a feature model, space is represented by combining primitives, and relationships among spaces are represented only if shared primitives are detected. So relationships between complex three-dimensional objects in space is difficult to be defined through the feature models. In this study, Navigable space-relation model(NSRM) is developed, which is topological data model for efficient representation of spatial relationships between objects based on the network structure.