Computer simulations are an important implementation to experimental methods working on polymer nanocomposites (PNCs), which have advanced properties because of their unique hierarchy microstructures. In this paper, different computer simulation methods applied to investigate the structures and properties of PNCs and the simulation predicted physical properties of PNCs are reviewed. The fundamentals of applying molecular dynamics simulation method to calculate different physical properties of PNCs are explained accompanied with detailed examples. The results can help to understand the progress on PNC field using simulation methods especially different-sized molecular dynamics simulation methods. Display omitted •Diverse kinds of computer simulation methods were reviewed and compared.•Simulation results of multiple physical properties were explored.•The fundamentals of calculating different physical properties using simulation methods were explained.