Hydrophobic membranes suffer from wetting and scaling when treating hypersaline brine using membrane distillation (MD). Thus omniphobic membranes with re-entrant surfaces have been developed by diverse modifications to enhance anti-wetting/scaling properties. However, those post-modifications usually sacrifice membrane permeability in spite of improved stability. In this work, omniphobic membranes were fabricated by decorating polyvinylidene fluoride (PVDF) nanofibrous membranes with different silica nanoparticles (SiNPs) followed by fluorination. Compared to unmodified nanofibrous and commercial PVDF membranes, both smaller SiNPs coated membrane #P-Min and larger SiNPs coated membrane #P-Max can perfectly sustain liquids with low surface tensions on their surfaces without wetting. In contrast to #P-Max with an oil contact angle of 136 ± 1°, #P-Min exhibited better oleophobicity with an oil contact angle of 152 ± 1°. In addition, the rigidity of their omniphobic properties was confirmed by testing in harsh conditions. Moreover, #P-Min successfully overcame the trade-off relation between membrane permeability and rejection with an enhanced MD flux due to more effective water evaporation area on membrane surface and a higher membrane porosity. While #P-Max was wetted by a hypersaline feed solution composed of 25 wt% NaCl, #P-Min could maintain a stable flux of 15 L m−2h−1 in a continuous 7-h MD operation, which proved its excellent performance for brine treatment. Furthermore, #P-Min exhibited less scaling tendency when feed was a saturated gypsum solution. Compared to #P-Max, the better anti-scaling properties of #P-Min should be due to its higher surface energy barrier, better slippery property and less solid-liquid contact area, which effectively impede crystal nucleation and attachment.