Calcium silicate hydrate (C–S–H) gels, the main binding phase of cement paste, determine the mechanical properties of cementitious materials. In order to obtain the cohesive force in C–S–H gel, molecular dynamics was carried out to simulate the uniaxial tension test on C–S–H model along x, y and z direction. Due to the structure and dynamic differences of the layered structure, C–S–H model demonstrates heterogeneous mechanical behavior. The calcium silicate layer, constructed by Ca–O and Si–O ionic-covalent bonds, has stronger cohesive force than that of interlayer H-bond network. In addition, composition influence on mechanical performance has been investigated by variation of the Ca/Si ratio. High calcium content, de-polymerizing the silicate chain structure in C–S–H gel, weakens uniaxial tension strength and elastic modulus in three directions. More water molecules penetration into the defective silicate region further reduces the mechanical properties of C–S–H gel at high Ca/Si ratio. Composition analysis at nano-scale can provide molecular insights on the cementitious materials design with different Ca/Si ratios.