The structure, composition and physical parameters of multilayer silicon carbide system synthesized by atom substitution method on the surface of low-dislocation single-crystal (111) oriented silicon were studied by Raman spectroscopy, ellipsometry, X-ray reflectometry, electron diffraction, IR spectroscopy, X-ray diffraction, AFM and profilometry. It was revealed that SiC films consist of layers, differing in SiyC composition, structure and thickness. The upper layers is a single-crystal 3C-SiC and the lower layers lying in depth of the substrate contain silicon carbide nanocrystals with a high degree of structure perfection and average size of 3–7 nm capable of preferential orientation (311), as well as large crystals (60–260 μm). The presence of cubic (3C-SiC) and hexagonal (mainly, 2H-SiC) polytypes with largest content of crystalline SiC phases in films with the composition closest to stoichiometric was established. In all samples there is carbon in super stoichiometric state, and its structure depends on the synthesis conditions.