Well-ordered self-assembled SrTiO3 thin film, as a template for complex oxide quantum wires, was fabricated on LaAlO3 (100) single crystal substrates with laser molecular beam epitaxy. The self-assembled growth was in-situ monitored by reflective high energy electron diffraction. The morphology evolutions of the films as a function of thickness were studied by ex-situ atomic force microscopy. As the thickness of the films increased from 3.875nm to 46.5nm gradually, the compressive stress-induced SrTiO3 films exhibited a periodic well-ordered ripple structure, which formed a unique nanoassembled template for the fabrication of quantum wires. Small angle X-ray scattering technique was employed to investigate the structure. Symmetric satellite peaks were discovered, indicating the well-ordered superstructure. In contrast, the similar superstructure was not observed during the growth of the tensile stress-induced LaAlO3 films on SrTiO3 substrates. The Compressive stress was considered as the main reason of the self-assembled growth, and systematical elucidation about strain mechanism was discussed. These results might provide an efficient method for the controllable formation of well-aligned template of quantum wire for complex oxide with desirable structure via proper modulation of strains.