Cement is the most widely used material in the world. Billions of tons of cement are consumed every year. Since cement manufacturing is one of the most carbon dioxide intensive industries, the high cement consumption becomes a serious problem. The demand for lower cement consumption and more reliable infrastructure requires development of high performance cementitious materials. With the advent of nanotechnology and emerging advanced computational tools, it is now possible to fundamentally understand and change the mechanics of cement-based materials from the nano scale up, providing key design guidelines for experiments. The main focus of this thesis is on the behavior of cement hydrate product, calcium silicate hydrate (C-S-H), and its hybrid derivative, Hexagonal Boron Nitride/C-S-H composite. C-S-H is the main source of strength and durability in all Portland cement concretes. Having a deeper understanding of the mechanical properties and deformation mechanisms of C-S-H is the basis for the development of new cementitious materials. Using molecular dynamics (MD) simulation, C-S-H is modeled by the layered tobermorite structure - a mineral analog of C-S-H. First, screw dislocations are simulated to evaluate the dislocations’ effect on the plastic deformation of C-S-H. The screw dislocations with different Peierls stress are identified, with which the plastic deformation of cement can be modulated. Next, by comparing various global deformations (e.g. shear, compression and tension) and a local deformation (e.g. nano-indentation), it is found that the global deformations lead to size-independent mechanical properties while the local deformation results in size-dependent mechanical properties at the nanometer scales. Three key mechanisms govern the deformation and thus mechanics of the layered C-S-H: diffusive-controlled deformation mechanism, displacive-controlled deformation mechanism, and local phase transformations with strain gradient. Together, these elaborately classified mechanisms provide deep fundamental understanding and new insights on the relationship between the macro-scale mechanical properties and underlying molecular deformations, providing new opportunities to control and tune the mechanics of layered crystals and other complex materials such as glassy C-S-H, natural composite structures, and manmade laminated structures. Finally, a hexagonal boron nitride (h-BN) reinforced cement is investigated for its high thermal and radiation-resistance. The rapid development of nuclear power plants (NPP) all over the world requires more advanced cementitious materials for radiation shielding and safety protection. Because of h-BN’s exceptional hardness, high thermal conductivity, and high neutron absorbing efficiency, the h-BN/C-S-H composite possesses higher strength, thermal tolerance and radiation-resistance. The radiation damage of h-BN, C-S-H, and h-BN/C-S-H composite are examined through a series of radiation cascade simulations. By assessing their strength degradation under different radiation dosages and temperatures, h-BN is found to help preserve more residual strength under extreme heat and radiation conditions. The proposed “thermal-radiation shock maps”, akin to thermal shock maps, for the first time uncovers the coupled effect of radiation and temperature on the strength of the structures, guiding science-based engineering of NPP concretes. This dissertation establishes a comprehensive understanding of cementitious materials at the atomic scale, providing fundamental understanding and guiding hypotheses for modern engineering of high performance cement-based materials.