Abstract: Long-distance water transfer projects, as important water conservancy infrastructure, undertake the critical task of trans-regional water resource allocation. In recent years, heavy rainfall flood events have occurred frequently. Compared with normal risks, super-standard heavy rainfall floods may cause damage paths that exceed engineering fortification standards. Once a project fails, serious economic and social problems may arise, and the operational safety of water transfer projects faces severe challenges. Therefore, it is necessary to conduct safety risk assessments of long-distance water transfer projects under super-standard heavy rainfall floods, which is of great significance for ensuring their safe operation. This paper takes long-distance water transfer projects under super-standard heavy rainfall flood conditions as the research object, and applies the WBS-RBS analysis method to construct a risk matrix from two dimensions: engineering structure and risk factors. Based on the composition of water conveyance structures, it identifies potential emergencies of different facilities under super-standard heavy rainfall flood conditions. According to the characteristics of risk sources, the risk factors are divided into three categories: external environment, human activities, and operation management. Drawing on literature review, accident statistics, and expert investigation, emergency events and risk factors are incorporated into a risk identification matrix to determine whether specific risks exist. From this matrix, the risk list of long-distance water transfer projects under super-standard heavy rainfall flood conditions is obtained. As many different structures are involved in the risk assessment, most existing weighting methods tend to focus on analyzing risk factors while neglecting the characteristics of engineering structures themselves and their surrounding complex environments. Under super-standard heavy rainfall flood conditions, clear differences emerge in the risk-bearing capacity and response mechanisms of structures. To quantify their relative importance within the project and to reduce deviations caused by expert subjectivity, an improved TOPSIS method based on the grey correlation coefficient is proposed. This approach objectively weights structures along the route according to multidimensional factors such as the degree of backward risk transmission, the severity of risk event consequences, the influence of rainfall area and terrain, the confluence conditions, and the number and operational status of upstream reservoirs. At present, most of the literature has primarily examined the probability of risk occurrence and the transmission mechanisms between risks. Risk ultimately affects the structures themselves. Therefore, considering the impact of the external environment, human activities, and operational management on the project, a forward-chain transmission framework is constructed to analyze the transmission mechanism of risks, quantify the influence of risk sources on structures, calculate the risk value of each facility, and evaluate the overall project risk based on the weighting results. The risk level classification standard is based on the risk matrix method, with the risk value defined in two dimensions and divided into four levels: low risk, moderate risk, high risk, and major risk. Taking 16 structures within a management office of a long-distance water diversion project as an example, this model was applied for risk assessment. The results showed that the water conveyance structures of the management office were, overall, in a low-risk state. To verify the practicality of the model, six structures were selected, and their external environmental risk deviation parameters were recalculated. The results were consistent with the actual engineering situation. The proposed risk assessment model provides technical support for the risk management of long-distance water transfer projects under super-standard heavy rainfall flood conditions and offers important reference value for ensuring their safe operation.