The applications of molecular simulation in supercritical carbon dioxide (S-CO2) and its mixtures are reviewed. First, an overview of physical properties of S-CO2 and CO2 models is given. Secondly, the accuracy of S-CO2 thermodynamic and transport properties calculated by different models is compared. It shows that Zhang’s model has relatively better global accuracy in calculating thermodynamic properties. EPM2, Zhang and Cygan models have similar accuracy when calculating transport properties based on equilibrium molecular simulation (EMD) method, but generally have higher deviations when calculating thermal conductivity. Therefore, EMD and non-equilibrium molecular simulation (NEMD) methods have been compared in calculating thermal conductivity. The results show that NEMD is better than EMD but the process is complicated. The structural properties are also discussed in this part. Thirdly, the applications of molecular simulation in S-CO2 binary organic, binary inorganic and multiple mixtures are reviewed. Finally, the summary and the prospect of future works are given.