In this study, composite membranes were fabricated via layer-by-layer (LBL) assembly of negatively charged silica aerogel (SiA) and 1H,1H,2H,2H-perfluorodecyltriethoxysilane (FTCS) on a polyvinylidene fluoride phase inversion membrane and interconnecting them with positively charged poly(diallyldimethylammonium chloride) (PDDA) via electrostatic interaction. The results showed that the PDDA-SiA-FTCS coated membrane had significantly enhanced the membrane structure and properties. New trifluoromethyl and tetrafluoroethylene bonds appeared at the surface of the coated membrane, which led to lower surface free energy of the composite membrane. Additionally, the LBL membrane showed increased surface roughness. The improved structure and property gave the LBL membrane an omniphobic property, as indicated by its good wetting resistance. The membrane performed a stable air gap membrane distillation (AGMD) flux of 11.22 L/m2 h with very high salt rejection using reverse osmosis brine from coal seam gas produced water as feed with the addition of up to 0.5 mM SDS solution. This performance was much better compared to those of the neat membrane. The present study suggests that the enhanced membrane properties with good omniphobicity via LBL assembly make the porous membranes suitable for long-term AGMD operation with stable permeation flux when treating challenging saline wastewater containing low surface tension organic contaminants.