In Nanjing Yangtze river tunnel project, quantitative engineering was applied to identify and prevent the risk. The numerical simulation method and supercomputing were employed to model the tunneling process in key sections. These key sections including departure and reception of shield machine, crossing flood levee, tunneling through river bed with shallow cover, interaction between two working shield machines, tunneling through composite soil layers were modeled according to the real geological profile. Quantitative analysis of the numerical results forecasted the risks in ground settlements, behavior of shield machine, and stability of cutting face, etc. The causes and consequences of the risks were discussed. After that, methods to prevent the risks were proposed, evaluated, and validated.