The phase change material (PCM), which is based on straight-chain alkanes, has received more and more attention for thermal management. To explore the mechanism of the thermal property of PCM from the microscopic scale, the molecular model of the PCM which consists of n-dodecane with amorphous structure is established in this study. The molecular dynamics (MD) simulation is performed with periodic boundary conditions and COMPASS force field. The melting temperature of n-dodecane is also determined by differential scanning calorimeter (DSC). The results show that the deviation of the isobaric heat capacity of the n-dodecane based PCM by MD method from the perviously reported value is 6.5%. The deviation of the simulated melting temperature of the PCM from the value from the DSC analysis is 7.6%. The simulated thermal conductivity of the PCM shows a slightly decreasing trend with pressure increasing, in a range of 0.1–0.4 W·m-1·K-1.