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A hybrid 3D spatial data structure for the integration of aboveground, ground and underground objects based on spatial cognition theory is proposed, which considers the space subdivision and topology completeness. Object-oriented method is used to abstract objects in real world which is defined into three levels. Geometry primitives and topology primitives are defined in this data structure. Topology is the option of the geometry. The geometry information can be coded in a binary method to store in the relation database. An experiment is designed to integrate the buildings, terrain, and geological stratification seamlessly. The data structure could express aboveground, ground and underground objects effectively.