The loading characteristics of underwater explosions and the dynamic behavior of bubbles are directly related to the charge structure. This study proposes a unique charge structure in a gas–liquid two-phase fluid domain. Numerical methods are used to investigate the effects of fluid layer thickness and gas–liquid ratio on underwater explosion shock wave load, bubble dynamics, and bubble pulsation load. The results show that the two-phase fluid layer significantly enhances the directional release of shock wave energy and bubble pulsation load. During the shock wave phase, a lagging wave effect appears in the liquid layer direction, causing a secondary high-energy shock, significantly increasing the specific impulse. The gas layer direction may form a pressure relief channel effect, enhancing the shock wave peak pressure. For the bubble motion phase, differences in the physical properties of the fluid layer medium lead to irregular bubble boundary movements, promoting bubble tearing and rupture. The gaseous medium converts the accumulated shock wave energy into the internal energy of the bubble, increasing its volume potential. Although this characteristic reduces the pulsation frequency, it significantly increases the specific impulse. Altering the fluid layer medium can control explosion loads and bubble movement, offering new insights for ocean engineering applications.