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Silane is known as an effective coating for enhancing the resistance of concrete to harmful acids and radicals that are usually produced by the metabolism of microorganisms. However, the mechanism of silane protection is still unclear due to its nanoscale attributes. Here, the protective behavior of silane on the calcium silicate hydrate (C–S–H) surface is examined under the attack environment of nitrate/sulfate ions using molecular dynamics simulations. The findings revealed that silane coating improved the resistance of C–S–H to nitrate/sulfate ions. This resistance is considered the origin of silane protection against harmful ion attacks. Further research on the details of molecular structures suggests that the interaction between the oxygen in the silane molecule and the calcium in C–S–H, which can prevent the coordination of sulfate and nitrate to calcium on the C–S–H surface, is the cause of the silane molecules’ strong adsorption. These results are also proved in terms of free energy, which found that the adsorption free energy on the C–S–H surface followed the order silane > sulfate > nitrate. This research confirms the excellent protection performance of silane on the nanoscale. The revealed mechanism can be further used to help the development of high-performance composite coatings.