The interaction of 4-sulfonatocalix[6]arene (SCX6) macrocycle with 1-alkyl-3-methylimidazolium type of ionic liquids possessing dodecyl, tetradecyl, or hexadecyl substituent was studied in aqueous solution at 298 K. Host-guest complexation promoted the spontaneous self-assembly into nanoparticles of 7:1 ionic liquid:SCX6 stoichiometry. Positively charged and stable nanoparticles were produced in solutions of 7-200-fold excess of ionic liquid as compared to the amount of SCX6. The negatively charged nanoparticles formed in solutions having 2-7 ionic liquid:SCX6 molar ratios evolved into larger species. The stability of the nanoparticles increased with the lengthening of aliphatic chain of the ionic liquid. Cryo-TEM experiments showed dense particles generally with spherical shape and multilayered structure, which has been confirmed by small-angle neutron scattering.