Flood disaster has become one of the most damaging natural disasters for the highway transportation all around the world, especially its destructive effects on highway infrastructures. In order to better understand the ruinous influence of flood disaster on highway transportation in China, this paper proposes an alternative evaluation index of highway flood disaster risk from three aspects, namely the disaster-causing factors, disaster-inducing environment, and disaster-bearing subjects. This paper also puts forward some targeted suggestions for the risk management, including two aspects: physical protection measurement and organization and management measurement. Moreover, this paper develops a highway flood disaster risk management system by using the ArcGIS technology.