Pore-scale particle migration in piping is the main reason of the suffusion-induced damage, which poses a significant threat to earth-rock dams. In order to investigate the micro-mechanism of piping seepage process, an improved fluid-solid coupling discrete element method is proposed in this paper. In this method, particles in a packed model are divided into coarse- and fine particle groups. Pores can be defined based on the coordinates of the coarse particles and the Delaunay triangulation algorithm. A pore density flow method is introduced to calculate the overall fluid pressure of each pore and the fluid flow via pore throats. Further, the drag force on fine particles inside a pore can be calculated according to the fluid velocities of the neighboring four pore throats. The proposed method was implemented in the discrete element software MatDEM, and was successfully used to simulate fine particle migration of piping, the particle loss process, and the related variation of permeability coefficient. The pore-jamming phenomenon during the fine particle migration is observed. The model provides an effective way for the numerical analysis and mechanism study of piping seepage process at the pore scale.