In this work we have developed a nanoscale composite protective preparation for car paint and varnish coatings. We developed methods to obtain SiO2-TiO2, TiO2-ZrO2, SiO2-ZrO2 and SiO2-TiO2-ZrO2 nanocomposites, which are crystallization centers for the formation of a nanoscale composite protective coating with certain morphology and roughness. The phase composition of the samples and stability in alkaline media were studied. It is shown that SiO2-TiO2-ZrO2 nanocomposites with a content of titanium dioxide from 8%–9.5% and zirconium dioxide from 0.5%–2% exhibit complete insolubility in a highly alkaline medium, allow to form uniform structure on paint and varnish coatings, and protect the car surface from exposure to ultraviolet radiation. We determined the optimal composition of the preparation components for the formation of a nanoscale composite protective coating with hydrophobic properties and a wetting contact angle of more than 120 degrees: tetraethoxysilane ≤ 10 vol.%., titanium tetraisopropylate ≥ 2 vol.% and plant resin ≥ 8 vol.% Practical approval of the developed preparation on BMW X6 showed a pronounced hydrophobic effect. Evaluation of the stability of the nanoscale composite protective coating to the washing process showed that the developed preparation is able to maintain its hydrophobic properties for more than 150 washing cycles.