Calcium silicate hydrate (C-S-H) is the most important hydration product of cement-based materials. In the nanostructure of C-S-H, structural water molecules are distributed in the interlayer region and determine the mechanical performance of C-S-H gel. In this study, C-S-H gels with different water contents expressed as the water/Ca ratio are characterized in the light of molecular dynamics. In order to study the influence of the water molecules, the structures of 12 C-S-H gel samples with water/Ca ratios from 0 to 0.95 are investigated. It is found that the penetration of water molecules transforms the C-S-H gel from an amorphous to a layered structure by silicate depolymerization as the water content gradually increases. The structures are then tested for mechanical properties by simulated uniaxial tension and compression. The mechanical tests associated with structural analysis reveal that the structural water molecules can greatly weaken the stiffness and the cohesive force by replacing the ionic-covalent bond with unstable H-bond connections. By studying the tensile failure mechanism of C-S-H gels at different humidity levels, the disconnecting role of the structural water molecules is comprehensively interpreted. Because the interlayer water molecules prevent reconstruction of the bonds between the Ca and the silicate chains, the plasticity of the C-S-H gels is reduced significantly in the change from a dry state to a saturated state. In addition, the compressive strength of a C-S-H gel in the saturated state is much larger than the tensile strength. This provides molecular evidence for the tensile weakness of cement paste. © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.