The thermophysical properties and microstructure of n-octadecane with crystalline and amorphous were investigated by employing the molecular dynamics (MD) simulation. The distribution of the end to end distance and bond torsion angle of the n-octadecane molecular chain and the mean square displacement and thermal conductivity before and after phase transition were also examined. MD simulation results indicates that the molecular chain conformation of amorphous n-octadecane in solid state is gradually changed from stretching to torsion by increasing temperature, and the chains will stretch out as the temperature rises in the liquid state. Compared with amorphous paraffin, the diffusion coefficient and the phase transition temperature of crystalline paraffin is lower than that of amorphous paraffin. The thermal conductivity of crystalline paraffin is much higher than that of amorphous paraffin. It is shown that improving the order degree of PCMs is an effective method to enhance their thermophysical properties.