The effect of pulsed laser annealing (PLA, i.e., action of nanosecond laser pulses in air atmosphere) on surface morphology, structure, chemical state, and electrical properties of thin films consisting of boron and carbon atoms was studied. The nanolayered В/С and mixed ВСx~3 thin film precursors (with a thickness ~110–140 nm) were created on sapphire substrates by using the pulsed laser deposition. Scanning electron microscopy and Raman scattering measurements indicate that the process of stratification of the multilayer B/C films dominated during PLA of the films. The outer layers were removed, and closer to the substrate, the B and C layers were preserved, and they were not mixed. For the mixed ВСх films deposited at elevated temperatures, the PLA treatment enhances ordering of initially amorphous film structure. At the stage of melting of these films, oxygen (from surrounded air) penetrated inside the top layer of the film leading to the formation of a multiphase structure from g-BCx and B-doped GO/rGO after solidification. Studies of the chemical state of elements in the irradiated film have shown that О atoms, which penetrated the under-surface layers of the film, facilitated the formation of new chemical bonds in the B–C–O system. The concentration of O atoms in the depth of the film could reach 8%. The preferential oxidation of boron in a homogeneous mixture of B–C–O atoms indicated that intercalation of carbon matrix could be due to the incorporation of not only O atoms, but also B–O molecules. The laser irradiated ВСх films have a relatively low resistivity (~1.6 mΩ·cm) and semi-metallic dependence on temperature in the range 4.2–300 К. The spatial distribution of conductivity zones after PLA has an irregular structure, and its pattern looks like sand dunes, indicating that the PLA treatment leads to mixing zones of high with those of lower conductivity. The contact-tip resistivity inside the areas of high conductivity of the ВСx/Al2O3 samples may be significantly lower than that of pure graphite.