Abstract Currently, manufacturing systems have become more and more complex, often involving multiple machines, systems and processes to produce workpieces. In order to facilitate comprehensive analysis and control of manufacturing processes, the integration of connections between machine level, system level, and process level in manufacturing process modeling is needed. However, traditional graph deep learning models are unable to take into account the heterogeneity of different machines in the system when modeling manufacturing systems. To address this problem, this paper proposes a new approach: modeling manufacturing systems using the heterogeneous graph neural network sample and aggregate algorithm based on cutting-edge Bayesian neural networks and graph deep learning. This method considers the connection between different manufacturing system levels, treats machine operations as nodes, and connects different nodes through material flow and operational similarity. The effectiveness of the method is demonstrated through its application to model an aero-engine blade production line. Extensive numerical experiments show that the proposed graph modeling method is effective in expressing the heterogeneity of different machines and multi-level manufacturing processes. By integrating machine heterogeneity into the modeling of a manufacturing system, it not only facilitates comprehensive analysis and control of the manufacturing process, but also lays the foundation for cost savings and productivity improvements in the manufacturing system.