Hydrated cement is one of the complex composite systems due to the presence of multi-scale phases with varying morphologies. Calcium silicate hydrate (C–S–H), which is the principal binder phase in the hydrated cement, is responsible for the stiffness, strength, and durability of Portland cement concrete. To understand the mechanical and durability behavior of concrete, it is important to investigate the interactions of hydrated cement phases with other materials at the nanoscale. In this regard, the molecular simulation of cement-based materials is an effective approach to study the properties and interactions of the cement system at the fundamental scale. Recently, many studies have been published regarding atomistic simulations to investigate the cement phases to define/explain the microscopic physical and chemical properties, thereby improving the macroscopic performance of hardened binders. The research in molecular simulation of cementitious systems involves researchers with multidisciplinary backgrounds, mainly in two areas: ① cement chemistry, where the hydration reactions govern most of the chemical and physical properties at the atomic scale; and ② computational materials science and engineering, where the bottom-up approach is required. The latter approach is still in its infancy, and as such, a study of the prevailing knowledge is useful, namely through an exhaustive literature review. This state-of-the-art report provides a comprehensive survey on studies that were conducted in this area and cites the important findings.