To clarify the origin of the nanostructure of ionic liquids (ILs), we have investigated two series of ILs 1-alkyl-3-methylimidazolium hexafluorophosphate (CnmimPF(6), n = 4-16, n is an alkyl-carbon number) and 1-alkyl-3-methylimidazolium chloride (CnmimCl, n = 4-14) using differential scanning calorimetry and X-ray diffraction techniques. The PF6 samples with n > 13 and the Cl samples with n > 10 exhibited the liquid-crystalline (LC) to liquid (L) phase transitions, as reported before. We found that both samples with smaller n also exhibited the LC to L transitions under supercooled states as far as the ionic motions were not frozen-in at the glass transition temperatures T-g. The T-g of the LC phase was close to that of the L phase, indicating that the characteristic length of the glass transition is shorter than that of the nanostructure. A low-Q peak due to the nanostructure in the L phase and a diffraction peak due to the layer structure in the LC phase appeared at almost the same Q positions in both samples. On the basis of the above results and some thermodynamic analysis, we argue that the nanostructures of ILs are essentially the same as the layer structures in the LC phases.