The crystallographic structure of thin Ga2O3 layers grown by metal–organic vapour phase epitaxy on Al2O3 substrate was analyzed by Rutherford Backscattering Spectrometry/Channeling (RBS/C) angular yield scans performed around the c-axis of as-grown Ga2O3. The measured widths and minimum yields of the scan curves for the Ga and O component were compared to calculations based on the continuum steering potential model. The results obtained are consistent with a crystal structure containing oxygen atoms arranged in a 4H hexagonal closely packed lattice and Ga atoms preferentially occupying octahedral interstitial sites in the 4H cells - a structure closely related to the ε-Ga2O3 polymorph. After high-temperature annealing remarkable structural transformation is detected via significant changes in the RBS/C spectra. This effect is related to the hexagonal-monoclinic, i.e., ε-β phase transformation of Ga2O3. Spectroscopic ellipsometry spectra of as-grown and annealed samples can be best fitted using a vertically graded single-layer B-spline model. Significant differences in the dielectric functions were found, showing bandgap reduction for long term annealing. These features are related to the ε-β polymorphic transformation, variation of the preferred crystallographic orientation upon annealing, and differences in residual strain and defect structure determined by the annealing conditions.