Due to its complexity at nanoscale, calcium silicate hydrate (C-S-H), the dominant binding phase in cement hydrates, is not yet completely understood. In this study, molecular dynamics was employed to simulate the hydration products at low and high calcium/silicon ratios. It was found that two morphologies of calcium silicate hydrate gels can be distinguished - a branched structure at low calcium/silicon ratios and an ellipsoid particle structure at high calcium/silicon ratios. Using virtual X-ray diffraction (XRD), nuclear magnetic resonance (NMR) and small-angle neutron scattering (SANS) techniques, the simulated structures were characterised, confirming that they show features of calcium silicate hydrate as revealed by experimental approaches. The short-range structures of calcium and silicon atoms and the distorted calcium tetrahedrons resemble the features of silicate glasses obtained from experiments, implying the amorphous nature of the local structure in calcium silicate hydrate gel. Furthermore, formation mechanisms for the two morphologies are proposed. In the hydration process, calcium ions play roles in depolymerising the silicate structure and preventing the amorphous network formation. Therefore, at low calcium/silicon ratios, the reaction is governed by silicate skeleton growth, but at high calcium/silicon ratio, aggregations of calcium ions and short silicate chains dominate.