Navigation networks are a common form of indoor map that provide the basis for a wide range of indoor location-based services, intelligent tasks for indoor robots, and three-dimensional (3D) geographic information systems. The majority of current indoor navigation networks are manually modeled, resulting in a laborious and fallible process. Building Information Modeling (BIM) captures design information, allowing for the automated generation of indoor maps. Most existing BIM-based navigation systems for floor-level wayfinding rely on well-defined spatial semantics, and do not adapt well to buildings with irregular 3D shapes, which can make cross-floor path generation difficult. This research introduces an innovative approach to generating 3D indoor navigation networks automatically from BIM data using image thinning, which is referred to as GINIT. Firstly, GINIT extracts grid-based maps for floors from BIM data using only two types of semantics, i.e., slabs and doors. Secondly, GINIT captures cross-floor paths from building components by projecting 3D forms onto a 2D image, thinning the 2D image to capture the 2D projection path, and crossing over the 2D routes with 3D routes to restore the 3D path. Finally, to demonstrate the effectiveness of GINIT, experiments were conducted on three real-world multi-floor buildings, evaluating its performance across eight types of cross-layer architectural component. GINIT overcomes the dependency of space definitions in current BIM-based navigation network generation schemes by introducing image thinning. Due to the adaptability of navigation image thinning to any binary image, GINIT is capable of generating navigation networks from building components with diverse 3D shapes. Moreover, the current studies on indoor navigation network extraction mainly use geometry theory, while this study is the first to generate 3D indoor navigation networks automatically using image thinning theory. The results of this study will offer a unique perspective and foster the exploration of imaging theory applications of BIM.