The effect of the annealing temperature on the optical and structural properties of the a-SiOx:H thin films prepared by gas-jet electron beam plasma chemical vapor deposition method was studied. Annealing was carried out at 600, 700, 800, 900 and 1000 °C for 4 h in oxidizing atmosphere. According to FTIR spectroscopy measurements, the oxygen and hydrogen concentration in the as-deposited films was 25 at.% and 2 at.%, respectively. The SEM image showed that the as-deposited material had column structure with a large number of vertical voids. As a result of annealing, the thickness of the films decreased by approximately 1.5 times for all samples. The value of refractive index at 650 nm decreased from 2.5 to 2.0 with the increase of the annealing temperature. The E04 optical gap decreased in comparison with the value of the as-deposited thin films for 600 °C and 700 °C, and increased for 800–1000 °C. For annealing at a temperature of 600 °C, the structure of the material changes insignificantly. A rearrangement in the structure of the matrix with the formation of amorphous silicon nanoclusters occurs at 700 °C and 800 °C. Annealing at the higher temperatures leads to transition from a material with amorphous nanoclusters to a material with nanocrystallites.