Underwater explosions have always been a hot topic in the field of ship protection. When explosives explode in offshore waters, the influence of seabed and structural boundaries on shock wave propagation and bubble pulsation will become more complicated. In this paper, a numerical simulation study of the underwater explosion between a deformable seabed and a rigid boundary is carried out. Firstly, the ABAQUS software was used to establish a numerical model by using the CEL method. The seabed was regarded as a heavier fluid, and the density ratio of the seabed and water was used to describe the characteristics of the seabed. The validity of the model was verified by comparison with experiments. Then, a series of numerical simulations were carried out by adjust the position of the explosive, the thickness of water medium layer, and the density of the seabed. The results show that: when the position of the explosive is close to the seabed and the rigid boundary, the bubble pulsation period is longer. The water jet and the pulsating pressure of the bubbles have a strong impact on the structure when the explosive is located near to 1 times the theoretical maximum radius of the bubble. As the depth of the water decreases, it can be observed that the bubbles transform from “ellipsoid” to “nipple-like”, and finally tear into upper and lower halves. When the thickness of water medium layer is 1 times the theoretical maximum radius of the bubble, the incident pressure waveforms of the bubble pulsation and the water jet near the structure are chaotic, which is caused by the “tear” phenomenon of the bubble. As the density of the seabed increases, the depth of the intrusion of the bubbles into the seabed becomes smaller and the shape of the bubbles becomes flatter. The research results of this paper can provide reference for the protection design of ships.