Water pollution has become a worldwide problem, partly due to the frequently happened oil spilling and oily wastewater discharge. As there are various forms of oil existing in water, the separation of oil-in-water emulsion is essential for thoroughly water purification. With the development of membrane technology, efficient emulsion separation has been achieved by constructing surfaces with super-wettability and high roughness on membranes. In this study, a facile method was established to fabricate a kind of highly hydrophilic and underwater oleo phobic polytetrafluoroethylene (PTFE) membranes. High efficiency, high flux and long-term stability were achieved during the oil-in-water emulsion separation process. The effect of surface wettability and membrane pore size on the demulsification and separation was studied. It was demonstrated that the emulsion separation is not only an interface problem, but also related to the pore structure of filtration membrane. Due to the high surface hydrophilicity and underwater oleophobicity, the membranes exhibited outstanding anti-fouling property and long-term performance. Our studies provided a theoretical guidance for the construction and application of emulsion separation materials for underwater use.