R-tree is very significant for spatial database. Moreover, levels of detail(LOD) is an important feature of 3D scene. This paper puts forward a logical model method for Integration of R-tree and LOD, which can efficiently realize the query function for LOD model and spatial objects. A database physical scheme is also designed to store R-tree and LOD. In the model, R-tree is extended into 3D space. This method can greatly improve performance of 3d visualization and management, which will be of great benefit to the practice of 3D GIS.