Owing to the limitations of visualization techniques in experimental studies and low-resolution numerical models based on computational fluid dynamics (CFD), the detailed behavior of oil droplets during microfiltration is not well understood. Hence, a high-resolution CFD model based on an in-house direct numerical simulation (DNS) code was constructed in this study to analyze the detailed dynamics of an oil-in-water (O/W) emulsion using a microfiltration membrane. The realistic microporous structure of commercial ceramic microfiltration membranes (mullite and αalumina membranes) was obtained using an image processing technique based on focused ion beam scanning electron microscopy (FIB-SEM). Numerical simulations of microfiltration of O/W emulsions on the membrane microstructure obtained by FIB-SEM were performed, and the effects of different parameters, including contact angle, transmembrane pressure, and membrane microporous structure, on filtration performance were studied. Droplet deformation had a strong impact on filtration behavior because coalesced droplets with diameters larger than the pore diameter permeated the membrane pores. The permeability, oil holdup fraction inside the pores, and rejection were considerably influenced by the contact angle, while the transmembrane pressure had a little impact on the permeability and oil hold-up fraction. The membrane structure, especially the pore size distribution, also had a significant effect on the microfiltration behavior and performance.