It is widely known that the accumulation of solid matter forming a cake layer on the membrane surface is one of the major limitations of the filtration performance in submerged membrane bioreactors (SMBR). This study is focused on the influence of the cake porosity of different particle microscopic packed structures on the filtration performance of hollow fiber systems. An integrated model based on the finite element method to simulate numerically the flow in an SMBR is presented. The model coupled the Navier–Stokes and Darcy Brinkman equations to simulate a complete filtration run. The cake growth took into consideration not only the deposition with local filtration velocity but also the effect of aeration scouring. A novel solution of mesh deformation was adopted to investigate transient cake growth along the fiber. Comparisons between simulations and experiments are in good agreement. The results show that a higher porosity particle packed structure causes non-uniform filtration and cake thickness but also higher permeate flux. Meanwhile, the proportion of cake resistance to total resistance increases with the decrease of porosity.