Shaped charge underwater explosions exhibit extreme destructiveness, involving large deformation, splashing, and fragmentation of metal jets; pulsation and jetting of explosion-induced bubbles; and structural rupture and perforation. These highly nonlinear phenomena pose significant challenges for numerical simulations. In this work, considering the superiority of Riemann solvers in handling discontinuities, a high-accuracy multiphase Riemann SPH is developed. To address excessive particle volume variation and non-uniform particle distribution, the Volume Adaptive Scheme (VAS) and particle shifting technique (PST) are utilized. Considering material constitutive equations, the damage mechanisms of the target structure subjected to the metal jet from a shaped charge is simulated to validate the accuracy of the developed model. Furthermore, for the penetration of the metal jet into a double-layer shell, the influences of the interlayer medium, liner geometry, and explosive type on the penetration behavior are systematically analyzed. Finally, to investigate the effects of the explosion-induced bubble following the metal jet, the interaction between the bubble and the perforated double-layer shell is performed under various characteristic parameters. The bubble motion patterns and loading characteristics are summarized. The findings provide valuable insights for optimizing shaped charge designs and assessing near-field structural damage in underwater explosions.