The South-to-North Water Transfer Project (SNWTP) in China is a considerable trans-basin water transfer project which can relieve the serious water resources shortage in northern of China and optimize water resources allocation. The construction of SNWTP has strategic importance to transfer the water from south to north and realize the target of water resources allocation. The operational management risks of SNWTP are discussed in this paper and the eastern route of SNWTP is studied as a case. The definition and connotation is given on the risk of operational management of SNWTP and the operational risk factors of SNWTP are distinguished. The index system of operational management risks is established. Considering the uncertainty of the risks of SNWTP, the risk evaluation model based on evidence theory is put forward. The countermeasures for the operational management risks of eastern route of SNWTP is brought up from the aspects of establishing risks management organization, risks management platform and emergency mechanism, technical methods and so on.