<p>Calcareous sand (CS), derived from marine organism debris, possesses unique morphological characteristics, influencing the mechanical and hydraulic behaviors under seepage conditions. However, the specific effects of different particle morphologies on the infiltration behavior remain unclear, particularly from a microscopic perspective. A fluid-particle system-based algorithm is employed, CFD-DEM (coupled computational fluid dynamics and the discrete element method), to investigate the influence of particle morphology of the porous skeleton on the migration and clogging processes of fine fragments under sustained hydraulic loading. This study focuses on understanding how different particle morphologies, including flaky, blocky, branched, and rodlike, affect the infiltration evolution and subsequent clogging. Through a series of numerical simulations, this study quantifies the evolution of infiltration performance across various skeletal configurations, investigates the variations in void structures induced by fine fragment infiltration, and analyzes the contact characteristics within shallow CS skeletons. The results reveal that various configurations based on particle morphology significantly affect the pore-throat network of the skeleton, including connectivity, tortuosity and volume, leading to sustained differences in contact behavior within the shallow skeleton. These differences, in turn, affect the infiltration performance, where the presence of flaky elements causes a marked decline in overall permeability. The results contribute to the broader understanding of seepage erosion in calcareous sand and offer the systematic evaluation of how morphological diversity affects infiltration mechanisms, highlighting the importance of considering particle morphology in the design of porous media for engineering applications.</p>