The effect of electron beam on the microstructures and phase transformation of nanostructured TiO2 heat treated at various temperatures for different time was studied by in-situ TEM and SAED. Anatase ex-situ heated at 250℃ and 360℃ transformed to rutile while irradiated by the electron beam. With the increasing sizes and distribution of the powders on the amorphous carbon, the process of phase transformation by the electron beam was encumbered. These evolutions may be due to the changes of vacuum atmosphere and the properties of powders.