The tungsten oxide nanoclusters were prepared by oxidation of epitaxialy grown tungsten thin film. The structure and morphology of tungsten and tungsten oxide nanoclusters were determined by RHEED (Reflection High-Energy Electron Diffraction) and AFM (Atomic Force Microscopy). The crystallographic structure and epitaxial relationships were evaluated. Annealing at the temperatures of 950 °C and 1150 °C gave rise to the tungsten clusters having (110) and (111) epitaxial planes, respectively. The two phases of tungsten oxide—WO2 and WO3—were found in dependence of oxidation conditions. The oxide clusters were epitaxially oriented on the α-Al2O3 substrate. The epitaxial orientations were deduced from the RHEED pattern and the surface distribution of clusters was characterised by AFM.