Silica aerogels are nanoporous materials with three-dimensional framework network structure. Silica aerogels have many unique properties such as high porosity, low density, low thermal conductivity and acoustical insulation properties. However, due to the poor mechanical performance of silica aerogels such as brittleness and high temperature instability, the large-scale commercial application of silica aerogels is limited. The thermodynamic properties of silica aerogels are related to their three-dimensional ligament network and pore structure. Exploring the relationship between microstructure evolution and macroscopic properties of silica aerogels is essential for improving their thermodynamic properties. Molecular dynamics (MD) simulations are an appropriate tool for the study of mechanical properties from the atomistic level. Based on the accurate potential, MD simulations have correctly predicted the power law that relates thermal conductivity and density. MD simulations also analyze aerogel structure from the atomistic level and predict their thermodynamic performance. The interatomic potential, pore structure generation, structural characterization, mechanical properties and thermal conductivity of the silica aerogels from the aspect of MD simulations are summarized. This work contributes to explaining the relationship between the structure and properties of silica aerogels from the atomistic level, which can provide a theoretical guidance for designing silica aerogels in terms of composition and structure.