The invention discloses a preparation method of a coating with a thiol compound as a transition layer, and belongs to the technical field of plasmas. According to the method, a sulfydryl-containing thin layer is adopted as the transition layer between the coating and a substrate; before the coating is deposited, the thin layer of 1-10 nm is deposited on the surface of the substrate by using a sulfydryl-containing monomer, wherein the sulfydryl at one end of the monomer reacts with the surfaces of copper, gold, nickel, epoxy resin and the like, so that a chemical bond is formed, the excellent binding property is kept, and the other end of the monomer is polymerized, and has the excellent binding property with the coating on the upper layer. According to the method for depositing the transition layer, the binding force of the coating and the substrate is greatly improved; according to the method , the environmental protection property is high, the deposition temperature is low, the speedis higher, and the controllability of the coating structure and the composition is high, and the selectivity of the monomer is high; the deposition efficiency is high, and the compactness of the obtained organic silicon nano-protection coating is remarkably improved; and the binding force obtained by the coating on different substrates can be improved by 30-50%.