The operation of super-long subsea tunnel is a extremly complex system project,has larger uncertainty and safety risk. The procedure of risk assessment was explained in detail,and its application on Bohai Bay subsea tunnel project was proposed as a case study in this paper. Firstly, lots of different risk factors of the subsea tunnel operation were identified systematically, which involved water damage,tunnel lining crack, tunnel freezing,tunnel lining corrosion,tunnel earthquake disaster,the air pollution inside the cave,tunnel fire and the train derailment accident. Then,those operational risks were analyzed and assessed by the confidence index method and analytic hierarchy process, and were classified and discussed gradually according to the risk acceptance criterion. Finally,some topics about risk assessment on the subsea tunnel operational risk needed to the further research were high-lighted here.