The major water transfer projects such as the East and Middle Routes of the South-to-North Water Transfer Projects are the main framework and artery of China's national water network. These long-distance water transfer projects have long routes and numerous buildings. The geographical environment and hydrological and meteorological conditions of the areas along the water transfer routes vary greatly and are complex and variable. In recent years, extreme meteorological events tend to be more frequent, more intense and more extensive. Extreme rainstorms and super standard floods occur occasionally, threatening the safe operation of these transfer projects. At the same time, with the economic and social development along the routes, some water transfer canal sections that deviated from originally urban areas have become urban canal sections. The impact of human activities and natural erosion and siltation of rivers have also led to changes in the external boundary conditions along the routes. In addition, with the increase of operating time, complex engineering geological canals and buildings are also facing their own risks of material aging and increase in hidden dangers and defects in anti-seepage and reinforcement foundations. It can be seen that long-distance water transfer projects face engineering safety risks caused by external environmental changes and internal behavior evolution during operation. To promote the high-quality development of the national water network in China, it is urgent to propose risk identification and assessment methods, and establish a full chain of risk control to ensure the safe operation of water network projects.A study was conducted based on the comprehensive risk assessment results of a major water transfer project in China. Various risk events faced by engineering safety during the operation period were analyzed, and the scheduling units between two control gates were determined as the risk assessment units. The processes of external risks transmission from left bank reservoirs, crossing rivers, etc. to water transfer projects were also analyzed. On this basis, a comprehensive risk assessment model for scheduling units based on analytic hierarchy process (AHP) was proposed. A beam type water conveyance aqueduct was selected as a case, and the identification of risk factors, risk event analysis, risk level classification standards, and risk assessment process for water conveyance buildings were explained. The scheduling unit where the aqueduct is located was taken as the assessment unit to conduct a comprehensive risk assessment using the AHP method. Finally, the risk assessment results of other scheduling units were also summarized, and the main reasons for causing high risks were discussed.The results indicate that the proposed method has good practicality. The risk value of the analyzed beam type aqueduct was 11.4, which is a relatively high risk (Level Ⅲ) due to changes in the crossing river, downward cutting of the cross-section riverbed, and insufficient burial depth of the canal piers caused by historical flood erosion. Based on the risk assessment results of the conveyance buildings, the risk value of the assessed scheduling unit was calculated. The risk of the evaluated unit project is 9.49, which also belongs to a relatively high risk (Level Ⅲ). The risk value of the water conveyance buildings is relatively high, at 10.28, with the main risk being the presence of diseases in the upstream reservoir and insufficient flood control standards, which poses a risk to the beam type aqueduct. After analyzing and calculating the risks of other scheduling units, the safety risks of the overall canal of the water transfer project mainly include the risks caused by the dam failures of the left bank reservoirs or flood discharges exceeding the flood control standards of the water transfer project, the risks of insufficient flow capacity of the crossing rivers, and the risks caused by poor discharge capacity of the left downstream buildings. Risk control measures were also proposed, mainly including the reinforcement of the left bank dangerous reservoirs and the improvement of their flood control standards.