In this study, we present a facile and scalable approach to fabricate omniphobic nanofiber membranes by constructing multilevel re-entrant structures with low surface energy. We first prepared positively charged nanofiber mats by electrospinning a blend polymer surfactant solution of poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) and cationic surfactant (benzyltriethylammonium). Negatively charged silica nanoparticles (SiNPs) were grafted on the positively charged electrospun nanofibers via dip-coating to achieve multilevel re-entrant structures. Grafted SiNPs were then coated with fluoroalkylsilane to lower the surface energy of the membrane. The fabricated membrane showed excellent omniphobicity, as demonstrated by its wetting resistance to various low surface tension liquids, including ethanol with a surface tension of 22.1 mN/m. As a promising application, the prepared omniphobic membrane was tested in direct contact membrane distillation to extract water from highly saline feed solutions containing low surface tension substances, mimicking emerging industrial wastewaters (e.g., from shale gas production). While a control hydrophobic PVDF-HFP nanofiber membrane failed in the desalination/separation process due to low wetting resistance, our fabricated omniphobic membrane exhibited a stable desalination performance for 8 h of operation, successfully demonstrating clean water production from the low surface tension feedwater.