Prior knowledge integration helps identify semantic entities and their relationships in a graphical representation, however, its meaningful abstraction and intervention remain elusive. This paper advocates a knowledge-inspired 3D scene graph prediction method solely based on point clouds. At the mathematical modeling level, we formulate the task as two sub-problems: knowledge learning and scene graph prediction with learned prior knowledge. Unlike conventional methods that learn knowledge embedding and regular patterns from encoded visual information, we propose to suppress the misunderstandings caused by appearance similarities and other perceptual confusion. At the network design level, we devise a graph auto-encoder to automatically extract class-dependent representations and topological patterns from the one-hot class labels and their intrinsic graphical structures, so that the prior knowledge can avoid perceptual errors and noises. We further devise a scene graph prediction model to predict credible relationship triplets by incorporating the related prototype knowledge with perceptual information. Comprehensive experiments confirm that, our method can successfully learn representative knowledge embedding, and the obtained prior knowledge can effectively enhance the accuracy of relationship predictions. Our thorough evaluations indicate the new method can achieve the state-of-the-art performance compared with other scene graph prediction methods.