The surface structure of SrTiO3(001) thin films homoepitaxially grown by PLD in step-flow mode was characterized using low temperature STM. It was found that one-dimensional (1D) TiOx-based nanostructures were formed on the thin film surface and their density increased with increasing thin film thickness. Most of the 1D nanostructures disappeared after a post-deposition annealing, indicating that this structure is metastable due to the nonequilibrium growth mode. The resulting surface after annealing exhibited similar features to that of a thinner film, having a domain structure with (2x1) and (1x2) reconstructions, but with fewer oxygen-vacancy-type defects. These results imply that the step-flow growth is likely to produce TiOx-rich surface and Ti deficiencies in the film. By the post-deposition annealing, the rich TiOx would diffuse from the surface into the film to compensate defects associated with Ti vacancies and oxygen vacancies, resulting in the stable surface structure with fewer oxygen vacancies. Thus, STM measurements can provide us with a microscopic picture of surface stoichiometry of thin films originating in the dynamics of the growth process, and can present a new approach for designing functional oxide films.