We report here the controlled formation of giant step bunching in the epitaxial growth of SrTiO3 thin film on vicinal MgO (1 0 0) substrates by on-axis radio-frequency (RF)-magnetron sputtering. We have studied the evolution of the surface morphology of such bunched steps by tuning the post-deposition annealing temperature. We demonstrate that the surface periodicity and reorganization of SrTiO3 nanostructures is widely enhanced under controlled post-annealing conditions in addition to Mg content diffusion in the SrTiO3 films. A morphology of facetted islands and bunched steps with extremely smooth terraces were obtained by post-annealing the SrTiO3 thin films at high temperatures. After a double post-annealing treatment at 900 °C and 700 °C, step bunching with a bunched step of fifteen-atomic unit cells and large terraced structures of about 1 µm width has been observed. The formation of these bunches of self-organized SrTiO3 nanostructures is of potential interest as templates for the growth of many functional materials.