To separate and collect microparticles such as cells, the behavior of particles in fibrous filters was investigated. It is essential to understand, in detail, the motion of particles in microscale flows, because Re is often small, and particles exhibit complex behaviors such as changes in relative position and spreading owing to hydrodynamic interactions. We calculated the motion of microparticles passing through the fibrous bed using the Stokesian dynamics method, in which hydrodynamic interaction is considered, theoretically. The fibrous bed was modeled by particles and five types of structures (a monolayer with fiber volume fractions ϕ of 3%, 4%, and 5%, and a bilayer with ϕ = 3−5% and 5−3%) were considered. Our numerical results showed that the particles moved in a complicated manner, and spread throughout the fibrous bed. It was found that the behavior of individual microparticles varied depending on the internal structure, although the average permeation velocity was primarily determined by the fiber volume fraction. This great dependence of the behavior of particle assemblage on the internal structure of the fibrous bed was caused by the individual particle motion under the influence of the layers in front of and behind them, owing to the hydrodynamic interaction.