Since amorphous oxygenated hydrocarbon (CO_xH_y) films are promising engineering materials a study of the structure and composition of the films depending on the conditions of synthesis is important for controlling of their physicochemical properties. Here, we used the methods of scanning and transmission electron microscopy, X-ray photoelectron, near-edge X-ray absorption fine structure, Fourier transform infrared and Raman spectroscopy to reveal changes in the chemical connectivity of CO_xH_y films grown on silicon substrates heated to 300, 500, and 700 °C using a supersonic flow of methane plasma. It was found that the CO_xH_y films, deposited at 300 and 500 °C, were mainly composed of the sp²-hybridized carbon areas with various oxygen species. A rise of the substrate temperature caused an increase of the portion of tetrahedral carbon atoms as well as carboxyl and hydroxyl groups. With growth of the substrate temperature, the film thickness reduced monotonically from 400 to 180 nm, while the film adhesion improved substantially. The films, deposited at lower temperatures, showed high hydrophilicity due to porosity and presence of oxygenated groups both at the surface and in the bulk.