Silica/montmorillonite hybrid nanoparticles were prepared to modify high‐density polyethylene which was used to fabricate wood/polymer composites (WPC). Surface modification of hybrids with γ‐methacryloxypropyltrimethoxysilane (MPTS) increased water contact angles from 10.7°to 88.1°and decreased the content of hydroxyl groups (42% relative OH content), indicating the successful grafting of MPTS. Compared with silica, the layered structure of montmorillonite (MMT) provided a better barrier (tortuous paths) for water penetration, and the incorporation of silica in hybrids provided more sites for MPTS grafting. Both of them resulted in the improvement on hydrophobicity for hybrids and WPCs. In the WPC system, some silicas in modified hybrids were not only dispersed in the polymer matrix but also penetrated into the cell wall of wood flours (WF) owing to the extruded process. The MMT in hybrids could mainly cover the WF surface. This distribution of hybrids could improve the WF mechanical strength and interfacial compatibility between the WF and polymer with the help of MPTS, resulting in enhanced mechanical properties of the composites. Compared with control (without nanoparticles), the tensile strength, impact strength, modulus of rupture and modulus of elasticity of the WPC with modified hybrids incorporation increased by 31%, 47%, 18%, and 28%, respectively.