With the continuous operation of the water transfer project, especially under the general trend of global climate change in recent years, extreme weather occurs frequently, and the project operation process will be tested by natural disasters, structural damage, electromechanical equipment failure, water pollution and other risks. Therefore, the risk management of the water transfer project is of great significance to ensure the long-term operation of the project. As one of the four largest cross-century projects in China, the operation risk of the South-to-North Water Transfer Project has attracted great attention. In this paper, a system dynamic model (SDM) for simulating real-time risk is presented. Based on the linear and directional characteristics of water transfer project and the known risk level of single buildings, DYNAMO language is embedded to connect the risks of various points on the line, and a model for real-time monitoring the risk changes along the line is constructed. The what-if analysis performed by the SDM shows the importance of human intervention to the deterioration and spread of dangerous situations in the process of engineering damage.