This dissertation investigates the mechanical properties and deformation mechanisms of cement at atomic level. Cement is the most popular building material in the world. Its hydrate product calcium silicate hydrate (C-S-H) is the main source of strength and durability in all Portland cement concretes. Having a deeper understanding of C-S-H would benefit the development of new cementitious material. Molecular dynamics (MD) simulation is able to reveal the behavior of C-S-H at atomic level that can not be obtained by theoretical and experimental study. Although attempts have been made to investigate the properties of C-S-H, its structure is too complex to be unraveled completely. The layered tobermorite structure, as a mineral analogy of C-S-H, together with a specially developed CSH-FF force field, is a proper atomic model for the simulation study of C-S-H. Based on which, screw dislocations are simulated to evaluate the dislocations’ effect on the plastic deformation of C-S-H. The screw dislocation with dislocation line perpendicular to the silica layer has larger Peierls stress, suggesting that plastic deformation is hard to occur if such screw dislocation dominates in C-S-H. Simulating global deformations (tension, compression, and shear) of the tobermorite structure demonstrates two deformation mechanisms: displacive and diffusive controlled deformation mechanisms. However, local deformation (nano-indentation) features phase transformation, with size effect arising due to strain gradient. Besides the atomic simulation of C-S-H, hexagonal boron nitride reinforced cement is modeled using a hybrid h-BN/tobermorite model. The h-BN/C-S-H composite possesses higher strength and higher radiation-resistance because of h-BN. The radiation damage of h-BN, C-S-H, and h-BN/C-S-H composite are examined through primary knock-on atom (PKA) simulation. By assessing their strength degradation under different radiation dose and temperature, h-BN is found to help preserve more residual strength from ~20% to ~70% in the most unfavorable conditions. All the findings of this study contribute to a comprehensive understanding of C-S-H at atomic scale, which is necessary to facilitate the development of new cement or cement-based material with high performance.