This paper investigates numerically the motion and deposition behaviors of micro- or nano-scaled particles in fluid passing three different kinds of square pores. The three kinds of square pores represent different pore structures in porous medium. The flow fields are numerically simulated by lattice Boltzmann method (LBM). The computation procedure code was validated by comparing the results with those of the previous works for the case of particle fluid passing a square block in a two dimensional channel flow. The results show that the dispersion of particles in three different square pore structures are much different, and vary with Stokes numbers for the same square pore even the Reynolds numbers are the same. In addition, the number and the position of deposited particles are analyzed. It shows that the deposition characteristics of each wall are mainly influenced by Stokes number, Reynolds number and the pore structure.