We present a numerical simulation method based on phase-field model and immersed boundary method for permeation of oil-in-water (O/W) emulsion through fibrous filter in coalescer process. First, the effects of the wettability of fibers and filter porosity on the coalescing dynamics are investigated by the simulations of O/W emulsions permeating through modeled fibrous filters. The simulation results reveal that the highly hydrophilic fiber surface brings about the generation of small secondary droplets during detachment from the filter. In addition, the large pore spacing promotes the formation of larger droplets but increases the number of uncoalesced droplets. Then, to represent a realistic flow field inside the fibrous filters during simulation, a numerical method that coordinates the filter structure obtained by X-ray CT imaging is developed. The simulation demonstrates that the arrangement of closely attached fibers at the permeate side surface of the filter enhances the formation of large droplets.