The composition, structure, and protective and hydrophobic properties of nanoscale films formed layer-by-layer in solutions of sodium dodecylphosphonate (SDDP) and vinyltrimethoxysilane or n-octyltriethoxysilane (OTES) on the zinc surface with different morphologies were studied by SEM, XPS, water contact angle measurements, and electrochemical and corrosion tests. The protective, hydrophobic properties of phosphonate–siloxane films on zinc and their stability in a corrosive media are determined both by the initial surface morphology and composition of the surface oxide layer, and by the nature of inhibitors. It was shown that preliminary laser texturing of the zinc surface is preferable than chemical etching to enhance the anticorrosive properties of the resulting thin films. The most stable films with excellent superhydrophobic and protective properties in atmospheres of high humidity and salt spray are formed on the zinc surface with fractal morphology during layer-by-layer passivation with SDDP and OTES.