In this work, the surfaces of poly (ethylene terephthalate) track-etched membranes (PET TeMs) with pore sizes of 670–1310 nm were hydrophobized with 2,2,3,3,4,4,5,5,6,6,7,7-dodecafluoroheptyl acrylate (DFHA) by photoinitiated graft polymerization. Attenuated total reflection FTIR spectroscopy (ATR-FTIR), scanning electron microscopy (SEM) coupled to an energy-dispersive X-ray spectrometer (EDX), and contact angle measurements were used to identify and characterize the TeMs. The optimal parameters for graft polymerization were determined as follows: polymerization time of 60 min, monomer concentration of 30%, and distance from the UV source of 7 cm. The water contact angle of the modified membranes reached 97°, which is 51° for pristine membranes. The modified membranes were tested for water desalination using direct contact membrane distillation (DCMD) method. The effects of membrane pore size, the degree of grafting, and salt concentration on the performance of membrane distillation process were investigated. According to the results obtained, it has been concluded that large pore size hydrophobic TeMs modified by using DFHA could be used for desalinating water.