The unstable mechanical behavior of soil particles during suffusion, including migration and clogging of fine particles in porous media, is prone to induce seepage catastrophes. Mechanical behavior of migratory fines and porous soils during suffusion is significantly influenced by the particle shape, which remains unclear. In this study, a coupled computational fluid dynamics and the irregular discrete element method (CFD-iDEM) framework is developed to investigate the migration and clogging mechanisms. A series of numerical simulations that consider spheres and irregular particles with different levels of aspect ratio are carried out to elucidate the microscopic origins of shape effects on clogging. Migratory fine particles are discharged from the grain inlet and enter the coarse particle skeleton by imposing a downward seepage flow. The subsequent migration and clogging phenomena and microscopic mechanisms are investigated. The results reveal that irregular particles present varying degrees of ability to develop clogging clusters, and spheres are more prone to traverse deeper into soil skeleton. The proposed CFD-iDEM method is able to reproduce macroscopic phenomena of saturated porous medium as well as to analyze microscopic origins of fluid–particle interactions, which contributes to practical guidance for engineering applications.