Structural perforation often occurs under underwater explosion (UNDEX) loadings, and understanding the interaction between UNDEX bubbles and perforated structures is important for evaluating secondary structural damage. In this study, a Riemann-based Smoothed Particle Hydrodynamics (SPH) method incorporating MUSCL reconstruction is employed to accurately capture strong discontinuities while minimizing numerical dissipation. To solve the issues of uneven particle distribution and drastic change of particle volume caused by the strong compressible characteristics of UNDEX bubbles, the particle shifting technique and particle volume adaptive algorithm are currently used to obtain uniform particle distribution and enhance numerical accuracy. Furthermore, an optimized initial particle distribution is utilized to significantly reduce the total number of particles and improve computational efficiency. In this work, the developed model is first validated by comparing the obtained SPH results and experimental results through the benchmark case. Subsequently, simulations of UNDEX bubble pair interacting with a perforated plate are performed, and the effects of standoff distance, bubble phase difference, and perforation diameter on bubble-induced loads are examined. Finally, the investigation is extended to the interaction between explosion bubbles and a perforated double-layer shell structure, in which the bubble motion patterns and associated loading characteristics are studied. The findings offer critical insights into the mechanisms of secondary structural damage resulting from underwater explosions.