The present research investigated the impact of the morphology change of titanate (TiO2) nanostructures on its tissue distribution and toxicity. The TiO2 nanotubes, rods, and ribbons were synthesized by the hydrothermal technique, and the morphology was adjusted by alteration of the hydrothermal duration time. The characterization techniques were X-ray diffraction, high-resolution transmission electron microscopy, dynamic light scattering, and the Brunauer–Emmett–Teller method for measuring the surface area. The intravenously administrated dose (5 mg/kg) was injected as a single dose for 1 day and consecutively for 42 days. The quantitative analysis of accumulated TiO2 nanostructures in the liver, spleen, and the heart was performed using an inductively coupled plasma emission spectrometer, and the organs’ toxicity was estimated by histopathological analysis. The prepared nanostructures exhibited differences in morphology, crystallinity, size distribution, surface area, zeta potential, and aspect ratio. The results revealed a tissue distribution difference between the liver, spleen, and heart of these nanostructures, the distribution order was the liver, spleen, and the heart for all TiO2 nanostructures. The toxicity was induced with different degrees. The nanotubes were the most harmful among the three formats. In summary, changes in the morphology of the TiO2 nanostructures change its distribution and toxicity.