Membrane distillation (MD) is considered a promising technology for desalination. In the MD process, membrane pores are easily contaminated and wetted, which will degrade the permeate flux and salt rejection of the membrane. In this work, SiC ceramic membranes were used as the supports, and an Al2O3 micro-nano structure was constructed on its surface. The surface energy of Al2O3@SiC micro-nano composite membranes was reduced by organosilane grafting modification. The effective deposition of Al2O3 nanoflowers on the membrane surface increased membrane roughness and enhanced the anti-fouling and anti-wetting properties of the membranes. Simultaneously, the presence of nanoflowers also regulated the pore structures and thus decreased the membrane pore size. In addition, the effects of Al2(SO4)3 concentration and sintering temperature on the surface morphology and performance of the membranes were investigated in detail. It was demonstrated that the water contact angle of the resulting membrane was 152.4°, which was higher than that of the pristine membrane (138.8°). In the treatment of saline water containing 35 g/L of NaCl, the permeate flux was about 11.1 kg⋅m−2⋅h−1 and the salt rejection was above 99.9%. Note that the pristine ceramic membrane cannot be employed for MD due to its larger membrane pore size. This work provides a new method for preparing superhydrophobic ceramic membranes for MD.