Determining the morphological distribution of hydrogen atoms in calcium silicate hydrate phase (C-S-H) is of great concern but challenging. In this work, based on the stoichiometric composition of (CaO)1.7(SiO2)(H2O)1.8, a series of amorphous Ca1.7•Si•(O)3.7-x•(OH)2x•(H2O)1.8-x models are constructed using Monte Carlo method, where x represents the molar number of dissociated H2O molecules (x∈0~1.8). A molecular dynamics simulation has been performed with the ClayFF force field. The analysis of Qn, radial distribution function (RDF), coordinate number (CN), mean chain length (MCL), mean square displacement (MSD), elastic modulus (M), and Young’s modulus (E) are used to explore the microstructure, hydrogen atom distribution and mechanical properties. The results demonstrate that the proportions of hydrogen atoms in Ca-OH, Si-OH, and H2O are about 26%~45%, 13%~22%, and 61%~33%, respectively. The calculated microstructure parameters and mechanical properties, especially for C-S-H models with x of 0.7~1.2, are in good agreement with those reported previously in theoretical and experimental works, indicative of the excellent rationality of our theoretical C-S-H models. The simulated results of this work provides a new strategy of constructing theoretical C-S-H model, which might be suitable for studying the doping behavior of metal oxides or metal salts in C-S-H.