Microgels with internal nanophase-separated structures were fabricated by surfactant-free emulsion copolymerization of N-isopropylacrylamide (NIPAm) and ionic liquid comonomers, namely, 1-vinyl-3-alkylimidazolium bromide (VIMnBr) with various lengths n of long alkyl side chain, in an aqueous solution at 70 degrees C using N,N'-methylenebisacrylamide as the cross-linker. Combined techniques of transmission electron microscopy, dynamic and static light-scattering, differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD), small-angle X-ray scattering (SAXS), and polarized optical microscopy were employed to systematically investigate the sizes, morphologies, and properties of the obtained microgels as well as the microstructures and phase transition of nanophases inside the microgels. The obtained P(NIPAm/VIMnBr) microgels are spherical with narrow size distributions, and the nanophases have a radius of about 8-12 nm and are randomly distributed inside the microgels. The cooperative competition of the hydrophilic quaternary vinylimidazole moieties and hydrophobic long alkyl side chains determines the thermal sensitive behavior of the P(NIPAm/VIMnBr) microgels. DSC and WAXD results reveal that the nanophases consist of the ordered alkyl side chains with a layered crystalline structure at low temperature, which exhibit a low melting temperature and a broad melting transition. SAXS results further show that the nanophases form a layered liquid crystalline structure at high temperature for the microgel suspensions and freeze-dried microgels.