Nanoemulsions are highly stable in the solutions. Separation of nanoemulsions is the most intractable problem in the wastewater treatment. The development of a low-cost, high-performance, bio-based membrane has been attempted to treat oily wastewater containing oil/water nanoemulsions. In this work, cellulose microfiltration membrane with inherent hydrophilic and underwater oleophobic behaviors were prepared by thermally induced phase separation (TIPS) using a lower critical solution temperature (LCST) system. High coagulation temperature enables rapid phase separation and prepares membrane with big pore size and loose pore structure, mainly controlled by the LCST-TIPS process. With the increase in the coagulation temperature from 10 °C to 50 °C, the water flux of cellulose membranes increased 7 times. Inherent hydrophilic and underwater oleophobic behaviors of cellulose makes the prepared cellulose microfiltration membranes displaying high efficiency in separation of oil/water nanoemulsions, including the lard and the food wastewater nanoemulsions with drop size in the range of 6–60 nm. Oil rejections are about higher than 99% to the peanut oil and the pump oil nanoemulsion and higher than 98% for the lard and the food wastewater nanoemulsions. These results demonstrate that the cellulose microfiltration membranes can be used for oil/water nanoemulsions separation in a green, economical, and efficient way.