Robust super-hydrophobic ceramic membranes consisting of layered structure Si2N2O grains and organosilane-derived inorganic nanoparticles were successfully fabricated and employed for membrane distillation. First, phase inversion and sintering method were used to prepare porous Si2N2O membranes. The slurry composition and sintering temperature were optimized to obtain a pure phase Si2N2O membrane with high bending strength, tailored average pore size, and high permeability. Then, the Si2N2O membranes were modified with organosilane-derived inorganic nanoparticles through ammonolysis and pyrolysis reactions. Due to the micro and nano-hierarchical rough structures and the presence of -Si-CH3 groups, the membranes showed super-hydrophobicity with a water contact angle of 152 ± 1°. Finally, the membranes were applied to desalinate seawater by sweeping gas membrane distillation. A stable water flux of 76 ± 0.9 L/(m2 day) with a salt rejection of > 99% was recorded during 30 h distillation test at 75 °C, demonstrating the stability and durability of the membranes.