A discrete element method (DEM) and computational fluid dynamics (CFD) based on a linear dipole model is proposed to simulate the clustering of fine particles in the sandy layer during the seepage process, and a numerical model of discrete porous media under the action of liquid seepage is further established. Specifically, the coarse particles are used to generate a porous medium skeleton. A linear dipole contact model is applied between the free fine particles to exert clustering driving force on the fine particles within a certain distance, and a rolling resistance linear model is applied between the coarse-fine particle contacts to reflect the effect of the unregular particle’s shape. Darcy’s law is used to describe the fluid flow in porous media at low Reynolds number, and the fluid-particle interaction is solved based on the two-way DEM-CFD coupling scheme. The results show that the numerical model can effectively generate and capture the clustering phenomenon of fine particles in porous media. Under fluid drag, compared to individual fine particles dispersed under the non-clustering condition, the agglomerated particle clusters are more likely to be trapped at the throat of the skeleton pore and form a blockage, retaining more solid components while also damaging the fluid flow performance of porous media. In the final state of the special case of the numerical model established, particle clustering reduces the loss of solid components by 76.50% and the average fluid permeability by 57.78% on the basis of non-clustering.