Membrane filtration has become firmly established as a primary process for ensuring the purity, safety and efficiency of treatment of water or effluents. Several researches have been performed to develop and design membrane systems in order to increase the accuracy and performance of the processes. In this study, a lattice Boltzmann method for the cake layer has been developed using particle dynamics based on an immersed boundary method and the cake layer formation process on membrane has been numerically simulated. Case studies including various particle sizes were also performed for a microfiltration process. The growth rate of the cake layer thickness and the permeation flow rate along the membranes were predicted. The results of this study agreed well with that of previous experiments. Effects of various particle diameters on the membrane performance were studied. The cake layer of a large particle tended to be growing fast and the permeation flow going down rapidly at the beginning. The layer thickness of a small particle increased constantly and the flow rate was smaller than that of the large particle at the end of simulation time.