Major water conservancy projects are important national infrastructures, whose damages caused by underwater explosions are noteworthy. Hence, centrifuge model tests and finite element simulations were used to study the effect of water storage level changes on the responses of dam. First, the similarity between the scaled model and the prototype in the hyper-gravity field was verified by numerical simulation. Next, based on the centrifuge model test at 50g, the effectiveness of the numerical simulation was verified. Then, a numerical simulation system was adopted to analyze the effects of underwater explosion on vibration and deformation of dam under different water storage levels. Results show that under the condition that the explosive equivalent and position remained unchanged, increasing the height of the water storage level caused the increase of the responses of the dam velocity and displacement. When the water depth exceeded 25 m, the peak velocity of multiple parts of the dam body exceeded the norm, and the dam might be damaged. Changes of the water storage level caused the impact energy of the dam to change, which affected the kinetic energy and strain energy of the dam. The energy change could be described by the spherical wave shock factor in this experiment.