Molecular dynamics (MD) is an important method for studying the molecular and atomic scale of cement (geopolymer)-based composites which provides an effective method for the optimal design of cementitious materials. In this paper, the research progress of MD simulation in Portland cement and geopolymer-based materials is discussed in detail, including molecular structure models of calcium silicate hydrate, calcium aluminosilicate hydrate, sodium aluminum silicate hydrate gel, and auxiliary experimental techniques. The basic mechanical properties of calcium silicate hydrate, calcium aluminosilicate hydrate and sodium aluminum silicate hydrate in Portland cement-based materials (CBM) and geopolymer-based materials are reviewed. In addition, the dynamic simulation of the interface between CBM and reinforcement materials such as rebar, synthetic fibers, plant fibers and nanoparticles is also discussed. Through the macroscopic experimental results of cement (geopolymer)-based materials and the performance analysis of an MD microscopic model, MD helps to better explain the macroscopic properties of materials, and can quickly and conveniently analyze the mechanical properties, transport properties and interface properties of composite materials, so as to improve the fine design of cement (geopolymer)-based materials. Existing structural models and force fields are affected by environment and time, and MD simulation shows great differences in application range and characterization ability. It is necessary to further study and reveal the internal mechanism for improving concrete performance through a large number of experiments and MD simulation, and lay a theoretical foundation for preparing the next generation of (super) high-performance concrete.