<p> Coral gravel soil, coral sand, and coral-derived mixed soil are common construction and building materials in coastal areas and islands, which are characterized by biologically formed fossilized sediments such as coral gravels (CG). The unique pore structures and irregular particle shapes of CG result in high porosity and significant breakage potential, influencing their mechanical properties and hydraulic behavior in engineering practice. However, the evolution of pore structures in CG during particle breakage and its impact on permeability remains poorly understood. This study employs a multi-scale analysis method, combining X-ray computed tomography and seepage simulations, to quantitatively investigate the evolution of pore structure and permeability in four types of CG: rod-shaped, branchlet, massive, and flaky during the particle breakage process. Test results categorized the internal pores of particles into intraparticle, blind, and through pores and demonstrated that as particle breakage occurs, intraparticle and blind pores decrease while through pores increase, leading to enhanced permeability. In the branchlet and flaky CG samples, intraparticle porosity decreases from 74.43% and 72.88% to 22.32% and 12.2%, respectively, while through porosity significantly increases with the progression of particle fragmentation. In addition, an exponential correlation between through porosity and permeability is established, supported by a regression model. This study proposes a framework for understanding multiscale pore evolution during particle breakage by analyzing changes in porosity and seepage behavior, improving the comprehension of the pore structure and hydraulic performance of fragmented granular materials. It provides valuable insights for the design and performance prediction of biological materials in offshore and geotechnical engineering applications.</p> Graphical Abstract