Structurally modified CMPO functionalized pillar[5]arenes in ionic liquid were found to be highly efficient, and radiolytically stable systems for the selective separation of thorium. The extraction was demonstrated to proceed via ‘cation exchange’ mechanism through [Th.L (NO3)]3+ species while the DFT calculation was used for understanding the optimized ligand structure and its complexation with Th4+ ion in ionic liquid. Oxalic acid was found to be successful for almost quantitative back extraction of thorium from CMPO functionalized pillar[5]arene complex in ionic liquid.