This study aimed to investigate and develop a cost-effective and superhydrophobic ceramic membrane for direct contact membrane distillation (DCMD) applications. Two types of mullite-based composite membranes were prepared via extrusion and sintering techniques. To create a small and narrow pore diameter distribution on the membrane surface, the dip-coating technique with 1 µm alumina was employed. The hexadecyltrimethoxysilane eco-friendly grafting agent was adopted to modify low-cost multilayer mullite-based composite membranes, transforming them from hydrophilic to superhydrophobic. The prepared membranes were characterized via field emission scanning electron microscopy (FESEM), energy-dispersive spectrometry (EDS), Fourier Transform Infrared Spectroscopy (FT-IR), X-ray diffraction (XRD), liquid entire pressure (LEP), contact angle, atomic force microscopy (AFM), porosity, and membrane permeability. The results of the prepared membranes validate the appropriateness of the material for membrane distillation applications. The optimized membrane, with a contact angle of 160° and LEP = 1.5 bar, was tested under DCMD using a 3.5 wt.% sodium chloride (NaCl) synthetic solution and Persian Gulf seawater as a feed. Based on the acquired results, an average permeate flux of 3.15 kg/(m2·h) and salt rejection (R%) of 99.62% were found for the 3.5 wt.% NaCl solution. Moreover, seawater desalination showed an average permeate flux of 2.37 kg/(m2·h) and salt rejection of 99.81% for a 20-h test without any pore wetting. Membrane distillation with a hydrophobic membrane decreased the turbidity of seawater by 93.13%.