Floods result in many problems, which may include damage to cross-river tunnels. The cross-river tunnel, as a new style of transportation, deserves a large amount of attention. In this paper, a large-scale cross-river tunnel model is proposed based on discrete element method (DEM). Micro parameters used in the model are calibrated by proposing a triaxial numerical model. Different in situ strata, high water pressures of normal flood-water levels and random vibration levels induced by running trains are taken into account to evaluate the dynamic characteristics of a high-stress tunnel in deformation and stress analysis. The results show that the upper half of the tunnel, including the concrete lining and the surroundings, is at higher risk than the lower half. Vibration waves transferring into the surroundings undergo an amplification process. The particles of the surroundings at the vault of the tunnel separate and move downward and then reassemble during the dynamic vibrations. The vibration levels, represented by particle accelerations, are lower under flood conditions than those under normal conditions. As train speed increases, the acceleration of the track and particles in the foundation increases, accompanied by a decrease in deformation.
