Highly crystalline TiO2 nanostructures were prepared through a facile inorganic acid-assisted hydrothermal treatment of hexagonal-structured assemblies of nanocrystalline titiania templated by cetyltrimethylammonium bromide (Hex-ncTiO2/CTAB Nanoskeleton) as starting materials. All samples were characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The influence of hydrochloric acid concentration on the morphology, crystalline and the formation of the nanostructures were investigated. We found that the morphology and crystalline phase strongly depended on the hydrochloric acid concentrations. More importantly, crystalline phase was closely related to the morphology of TiO2 nanostructure. Nanoparticles were polycrystalline anatase phase, and aligned nanorods were single crystalline rutile phase. Possible formation mechanisms of TiO2 nanostructures with various crystalline phases and morphologies were proposed.