The topmost atoms of TiO2-terminated SrTiO3(001) annealed at temperatures between room temperature and 800 degrees C in ultra high vacuum (UHV), have been studied by means of in-situ coaxial impact collision ion scattering spectroscopy (CAICISS). Both time-of-flight spectra at the incident angle of 45.0 degrees along [(1) over bar 00] azimuth and of 35.3 degrees along [(1) over bar (1) over bar 0] azimuth revealed Ti and weak O peaks and no Sr peak at 150 degrees C, which means that the topmost layer at 150 degrees C is terminated by TiO2-plane, completely. On the other hand, as increasing the substrate temperature, Sr peak began to appear above 400 degrees C. This Sr peak intensity from both directions was drastically increased with elevating the substrate temperature. This indicates that the topmost O and Ti atoms desorb from the surface at the higher substrate temperature. The ratio Sr/Ti corresponds to the amount of the topmost oxygen or titanium vacancies due to the desorption. It was found that 40% of the topmost oxygen atoms and 32% of the topmost titanium atoms desorb from TiO2-terminated SrTiO3(001) surface at 800 degrees C. The activation energies for oxygen and titanium desorption were 0.28eV and 0.40eV, respectively.