It was found in this study that fluorinated microporous carbon aerogels with enhanced hydrophobicity could be successfully prepared by direct fluorination to separate water-in-oil emulsions at high flux. The fluorinated carbon aerogel (F-CA) surface treated by the fluorination method had a water contact angle of 151.2° and could immediately absorb oil. In addition, the unique network structure of F-CA and its hydrophobicity allow surfactant-stabilized water-in-oil emulsions to be effectively and simply separated under gravity without requiring external forces such as vacuum or pressurization. The network structure of F-CAs consists of randomly connected spherical particles that form fluorinated permeation channels, which induce high flux during emulsion separation. The F-CA spherical particles have nanosized pores and high hydrophobicity, which repel and trap water droplets to increase the separation purity. Therefore, F-CA exhibited excellent performance, such as high filtrate purity (up to 99.9954%) and flux (up to 11,710 L/m2h). Furthermore, F-CA reusability was demonstrated as it did not lose its hydrophobicity and maintained its performance even after repeated use. This type of aerogel has great potential to be utilized throughout various environmental fields, including oil remediation.