The super-hydrophobic nature of surfaces is greatly dependent on the interfacial molecular structure of coating materials. In this study, to understand the structure, dynamics and interfacial behavior of hydrophobic coating, molecular dynamics is utilized to study the capillary transport of water molecules through the nanometer channel of calcium silicate hydrate (C-S-H) with the interior surface impregnated with silane. The C-S-H surface is coated by connecting the bridging silicate tetrahedron with an oxygen-containing group in isobutyl-triethoxysilane (C10H24O3Si) with a silane molecule coverage rate ranging from 25% to 100%. We demonstrated that the silane coating with a coverage exceeding 25% can effectively inhibit the water molecule and detrimental ion invasion in the gel pore. The grafted silane groups reduce the number of non-bridging oxygen atoms in the surface silicate chains that provide plenty of sites to accept the H bonds from the surface water molecules. This results in the reduction of the dipole moment of the surface water molecules and transforms the hydrophilic C-S-H substrate to hydrophobic. The silane molecules, immobilized by the Si-O-Si bond on the C-S-H substrate, are protruded to the gel pore with the hydrophobic tail of branch-like isobutyl groups. It transforms the smooth surface to a lotus-leaf-like rough surface with distributed nanoscale papillae. The isobutyl groups, freely vibrating and rotating, further blocks the connectivity of the transport channel and weakens the interaction between penetrated ions and C-S-H substrates. Furthermore, spatial correlation analysis demonstrates that the immobilized silane molecules disturb the tetrahedron distribution of water molecules in the gel pore and break the hydration shell of the counter Ca ions that associate with less water molecules. The dramatic degradation of the time correlation function for the surface solution species in the presence of isobutyl-triethoxysilane exhibits that the coated C-S-H surface can repel the surface water molecules and calcium ions by weakening the H bond and the Ca-O ionic bond strength. These nanostructure results provide guidance for the construction of artificial super-hydrophobic surfaces and the design of cementing materials with controllable wettability.