The design process of heating, ventilation, and air conditioning (HVAC) systems is complex and time consuming due to the need to follow design codes. Since the design standards are not fixed, the final outcome often depends on the designer’s experience. The development of building information modeling (BIM) technology has made information throughout the building lifecycle more integrated. BIM-based forward design is now widely used, providing a data foundation for combining HVAC system design with machine learning. This paper proposes an unsupervised learning method based on deep graph generative models to uncover hidden design patterns and optimization strategies from the design results. We trained and validated four deep graph generative models—GAE, GNF, GAN, and diffusion—using HVAC system terminal pipeline layout data. Accuracy and precision metrics were used to compare the generated designs with automated forward design solutions, assessing the models’ ability to capture both local variations and broader changes in design logic. A graph-neural-network-based evaluation method was employed to measure the models’ capacity to detect changes. The results indicate that all four models achieved prediction accuracies exceeding 90% and precision rates above 75%. The models effectively captured both local modifications made by designers and global design changes, showing greater sensitivity to global layout adjustments than to local updates. When comparing the results generated by deep graph generative models and the actual design, it is obvious that the accuracy of the predictions varies significantly due to the complexity of the test buildings.