In this paper, preliminary built and put into operation in the middle route of South-to-North Water Transfer Project in Beijing section as an example, the use of project risk management theory, through the risk identification method after comparison and analysis, put forward the risk stage identification method. In the use of expert investigation, Delphi method to the risk identification, the system is decomposed into several subsystems, using failure mode effect analysis principle, further identify the system failure mode, failure, failure parts, so that each subsystem risk factors, and finally summarized the Mid-route of South-to-North Water Transfer Project of Beijing section engineering risk recognition framework.