In this study, a superhydrophobic Cu gauze (SCG) was prepared and used for the phase separation of non-aqueous FAME-glycerol mixtures. The separation of three FAME/glycerol mixing scenarios in biodiesel production, blending, emulsion, and floating FAME, was conducted in batches. Results confirmed glycerol-repellence and FAME-attraction of the obtained SCG. The separation efficiency of FAME/glycerol blending mainly depended on impurities that affected glycerol solubility in FAME. Emulsion separation was determined by the relative size between the dispersed glycerol droplets and SCG mesh. Floating FAME on the glycerol surface was completely collected with a sponge enwrapped by SCG with 99.12% recovery. The continuous separation of FAME/glycerol mixture with SCG produced qualified biodiesel product with 0.0166 wt% glycerol content and phase separation efficiency reached 98.26%. This work broadens the possible application of superhydrophobic surfaces to non-aqueous systems.