In this Letter we report on controllable transition of aggregated γ-Cyclodextrins (γ-CDs) nanostructures by tuning the concentration of a long chain ionic liquid, 1-dodecyl-3-methyl imidazolium chloride (C 12mimCl) added to the aqueous solution of γ-CDs. The gradual increase in concentration of C12mimCl first results in the breaking of γ-CDs aggregates by the formation of inclusion complexes with C 12mimCl and then self-organizes into a new supramolecular aggregate. This spontaneous transition from one nanostructure to another has been established by spectroscopic and microscopic studies. It is worth to mention that addition of 1-octyl-3-methyl imidazolium chloride (C8mimCl) does not lead to any such transition. © 2014 Published by Elsevier B.V.