The high-temperature morphology of supported liquid membranes (SLMs) prepared from perfluorinated membranes such as Nafion and Hyflon and hydrophobic ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BMI-TFSI) has been investigated by small-angle X-ray scattering (SAXS). Proton conductivity results of SLMs before and after leaching show an increase in conductivity with temperature up to 160 °C in an anhydrous environment. DSC results show that crystallites within perfluorinated membranes are thermally stable up to 196 °C. High-temperature SAXS results have been used to correlate structure and morphology of supported liquid membranes with high-temperature conductivity data. The ionic liquid essentially acts as a proton solvent in a similar way to water in hydrated Nafion membranes and increases size of clusters, which allow percolation to be achieved more easily. The cation of the ionic liquid interacts with sulfonate groups within ionic domains through electrostatic interactions and displaces protons. Protons can associate with free anions of the ionic liquid, which are loosely associated with cations and can transport by hopping from anion sites within the membrane. The ionic liquid contributes to proton conductivity at high temperature through achievement of long-range ordering and subsequent percolation.