Methyl linolenate (C18-3) is a type of unsaturated fatty acid methyl ester with high biological activity. Membrane separation of C18-3 from tallow seed oil methyl ester by supported ionic liquids membranes (SILM) containing carrier Ag+ was successfully achieved in this study. The interaction between Ag+ and C18-3 was explored by density functional theory (DFT). High selectivity to C18-3 was mainly due to the pi/inverse pi complexation interactions between Ag+ and C=C bonds. The effects of ionic liquid structure, carrier Ag+ concentration, adjacent phase flow rates and membrane pore size on permeability and selectivity to C18-3 were examined. The existence of 1-hexene in the stripping phase and carrier Ag+ can facilitate C18-3 transport. Good separation performance was achieved by the 0.45 mu m nylon membrane impregnated with ionic liquid [BMIm] BF4 containing AgBF4. C18-3 was enriched from 16.7% in the feed phase to higher than 75% in the product. Moreover, adding a hydrophobic PVDF protective membrane to form a composite membrane was an effective method to increase the SILM stability and membrane lifetime by about twice compared with a single nylon membrane.