Abstract In recent years, research articles involving molecular dynamics simulations of construction materials have grown significantly in number. The growth reflects an emerging need to understand microscopic physical and chemical processes, which are fundamental to further improve the macroscopic performance of construction materials. Nano-engineering, as a concept about manipulating material structures for creating new materials or modifying existing materials, highly depends on the understanding of materials at the nanoscale, where molecular dynamics simulation becomes an effective and powerful investigation tool. In this paper, the applications of molecular dynamics simulations in understanding the fundamental deformation mechanism of various construction materials including concrete and cement, fiber-reinforced polymers and related bonded systems upon nano-engineering approach are presented. In addition, the study on nature materials towards their structural morphology and functions at the atomistic level is illustrated so as to inspire the future development of advanced construction materials. The challenges and innovations associated with nano-engineering are also discussed.