Flood control risk is one of the main risks affecting the safe operation of large-scale water transfer projects. Systematically identifying the flood control risk in the project and carrying out risk classification and hierarchical management are problems for project managers. Based on the theory of system and risk assessment, this paper starts with the various risk sources and risk events involved in the whole process of the flood disaster chain, the risk of flood disaster factors, the exposure of the disaster-bearing body, and the vulnerability of the disaster-originating environment are combined. Then, we systematically and comprehensively identify the flood control risks of a large-scale water transfer project, which are divided into four types of risk elements: rainfall–runoff; confluence and flow capacity; the geological characteristics of canal section; economic and social layouts. Specific risk factors are identified for each type of risk element, and a flood control risk evaluation index system for a water transfer project is proposed. According to the framework of the analytic hierarchy process (AHP), a quantitative assessment of comprehensive flood control for water transfer projects is carried out. Taking the middle route of the South-to-North Water Transfer Project in China as an example, this paper evaluates the integrated flood control risks of 39 engineering units, identifies six units with higher risk levels, analyzes the causes, and suggests engineering and non-engineering countermeasures to prevent and reduce the occurrence of risk accidents. This method is not only used for comprehensive flood control risk assessment and risk management in the operation and management stage of the large-scale inter-basin water transfer project, but also has a reference value in considering the optimal layout of the project water transmission line from the perspective of flood control in the planning and design stage.
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