We report on a dramatic effect of the surface reconstruction of the substrate on thin film growth. We prepared two types of surface reconstruction, namely 2 × 1 and (√13 × √13)-R33.7° reconstructions, by annealing the SrTiO3(001) substrates in ultrahigh vacuum (UHV) and an oxygen environment, respectively. Subsequent co-depositions of Fe and Se atoms onto the 2 × 1 and (√13 × √13)-R33.7° reconstructed SrTiO3 surfaces lead to the growth of thin films of distinct six-fold and four-fold symmetry, respectively, under nominally the same growth conditions. Based on in-situ angle-resolved photoemission spectroscopy (ARPES) measurements of the electronic structure, we ascribe the aforementioned two types of thin film to the reported hexagonal and tetragonal phases of FeSe, respectively. The observation of the growth of hexagonal FeSe on the tetragonal SrTiO3 surface with a 2 × 1 reconstruction is unexpected, the underlying mechanism of which remains an outstanding puzzle. Our finding adds a new dimension to the material phase control via the choice of surface reconstruction of the substrate used for thin film growth.