Mechanisms of hydrogen bonding and molecular structure in the C-S-H are investigated by combining results of 29Si, 1H solid SSNMR analysis and first principle calculations. First principle calculations for 1H chemical shifts are used to correlate the observed 1H SSNMR spectra with the underlying structure of various hydrogen bonds between different silicon moieties and hydrogen groups in the C-S-H gels. The results show that strong hydrogen bonds are formed between water and terminal silicate sites or silanols, between adjacent terminal silanols and terminal silicate sites, between water or terminal silanols and hydroxyl groups bonded with interlayer calcium ions. Strong hydrogen bonds are favored to form in C-S-H with high Ca/Si molar ratios. The hydrogen bonding in terminal silicate sites is stronger than those in the paring or bridging silicate sites. New insights into the changes of basal spacing, Ca/Si ratio and H2O/Si ratio of in the molecular structure of C-S-H are presented based on the mechanism of hydrogen bonding.