In this study, a multi-layer core-shell nanoparticle with multiple functions was prepared by a two-step process. First, the hydrolysis-condensation reaction of 3-methacryloxypropyl trimethoxysilane (MPS) and tetraethoxysilane (TEOS) was performed on the surface of the pre-synthesized SiO2 nanoparticles to form the MPS/SiO2 core-shell nanoparticles. Second, the copolymerization of octadecyl methacrylate (ODMA) monomers with CC bonds was carried out on the surface of MPS/SiO2 nanoparticles to form PODMA/MPS/SiO2 multi-layer nanocomposite. The hybrid nanocomposite could be used directly as the thermostable hydrophobic coatings. The prepared coatings not only were hydrophobic with the water contact angle greater than 130°, but also exhibited high heat resistance. Moreover, the hybrid nanocomposite could also be used as nano viscosity depressants for crude oil. The viscosity of crude oil could be reduced more than 80%. Owing to these good practical advantages, the PODMA/MPS/SiO2 hybrid nanocomposites may have some potential applications in practical industrial production.