The hydrophobic membranes have been widely explored to meet the membrane characteristics for the membrane distillation (MD) process. Inorganic metal oxide nanoparticles have been used to improve the membrane hydrophobicity, but limited studies have used nano clay particles. This study introduces halloysite nanotube (HNT) as an alternative material to synthesis a hydrophobic poly(vinylidene fluoride) (PVDF)-HNT membrane. The PVDF membranes were fabricated using functionalized HNTs (e.g., carnauba wax and 1H,1H,2H,2H-perfluorooctyl-trichlorosilane (FOTS)). The results were determined by Fourier transform infrared-attenuated total reflection, scanning electron microscope, goniometer and porometer to determine the desired hydrophobic membrane for direct contact membrane distillation (DCMD). The addition of FOTS-HNT (fs-HNT) and carnauba wax-HNT (fw-HNT) in the PVDF membrane enhanced the water contact angle (CA) to 127° and 137°, respectively. The presence of fw-HNT in the PVDF membrane exhibited higher liquid entry pressure (LEP) (2.64 bar) compared to fs-HNT in the membrane matrix (1.44 bar). The PVDF/fw-HNT membrane (Pfw-HNT) obtained the highest flux of 7.24 L/m2h with 99.9% salt removal. A stable permeability in the Pfw-HNT membrane was obtained throughout 16 h of DCMD. The incorporation of fw-HNT in the PVDF membrane had improved the anti-wetting properties and the membrane performance with the anti-fouling effect.