In a three-dimensional topological insulator Bi2Se3, a stress control for band gap manipulation was predicted but no systematic investigation has been performed yet due to the requirement of large external stress. We report herein on the strain-dependent results for Bi2Se3 films of various thicknesses that are grown via a self-organized ordering process. Using small angle X-ray scattering and Raman spectroscopy, the changes of d-spacings in the crystal structure and phonon vibration shifts resulted from stress are clearly observed when the film thickness is below ten quintuple layers. From the UV photoemission/inverse photoemission spectroscopy (UPS/IPES) results and ab initio calculations, significant changes of the Fermi level and band gap were observed. The deformed band structure also exhibits a Van Hove singularity at specific energies in the UV absorption experiment and ab initio calculations. Our results, including the synthesis of a strained ultrathin topological insulator, suggest a new direction for electronic and spintronic applications for the future.