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 α-alumina 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 hold-up 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.