In recent conflicts and terrorist attacks, dams have increasingly been targeted by warheads. This study aims to examine the loading characteristics and damage effects of underwater explosions caused by warheads on concrete gravity dams. Specifically, a typical concrete gravity dam with a height of 60 m and the BLU-109/B warhead with 324 kg of TNT were selected as the subjects of analysis. Firstly, the finite element analysis method for prototype concrete gravity dams against underwater explosions with cubic and cylindrical charges was established and verified by comparing the experimental and simulated incident pressure-time histories from underwater explosion tests with two types of charges, as well as the damage modes of reduced-scale dam specimens. Secondly, numerical simulations were conducted on prototype concrete gravity dams against warhead underwater explosions. The loading characteristics considering both the blast wave and bubble pulsation phases, as well as the damage modes of the dam under the cylindrical charge, i.e., identical to the warhead shape, were examined. Furthermore, a comparison with the commonly adopted cubic charge was conducted. Finally, the influence of standoff distance on the damage modes of dam was discussed. It shows that the loading distribution induced by cylindrical charges exhibits an obvious directionality in comparison to cubic charges. Consequently, the damage modes and degree demonstrate significant differences. As the standoff distance of the warhead increases, the damage degree of the dam generally shows an initial increase followed by a decrease, with a critical turning point at 6.2 m.