Hydrophobic metakaolin-based flat sheet membrane was developed via phase inversion and sintering technique and modified through 1H,1H,2H,2H-perfluorooctyltriethoxysilane grafting agents. The prepared membrane was characterized by different techniques such as XRD, FTIR, SEM, contact angle, porosity, and mechanical strength. Their results indicated that the wettability, structural, and mechanical properties of the prepared membrane confirm the suitability of the material for membrane distillation (MD) application. The prepared metakaolin-based flat sheet membrane acquired hydrophobic properties after surface modification with the water contact angle values of 113.2° to 143.3°. Afterward, the membrane performance was tested for different sodium chloride aqueous solutions (synthetic seawater) and various operating parameters (feed temperature, feed flow rate) using direct contact membrane distillation (DCMD). Based on the findings, the prepared membrane at metakaolin loading of 45 wt.% and sintered at 1,300 °C was achieved the best performance with >95% salt rejection and permeate flux of 6.58 ± 0.3 L/m2 · h at feed temperature of 80 °C, feed concentration of 35 g/L, and feed flow rate of 60 L/h. It can be concluded that further optimization of membrane porosity, mechanical, and surface properties is required to maximize the permeate flux and salt rejection.