The straight chain n-alkanes based paraffin phase change materials (PCM) have been widely investigated by experimental and numerical methods. This paper presents a study from molecular point of view to discuss the self diffusion and heat capacity of n-alkanes and their binary mixtures based PCM with molecular dynamics (MD) simulation method. Four PCM systems, n-nonadecane, n-tetracosane, n-nonadecane and n-tetracosane (1/1) and n-nonadecane and n-tetracosane (3/1), were constructed with amorphous structure and periodic boundary conditions. The results showed that the phase transition behaviors of the PCM could be determined according to the variation of simulated self diffusion coefficient and isobaric heat capacity. Comparisons of isobaric heat capacity between the MD and experimental results showed reasonable agreement below 353 K. The strength and width of radial distribution functions indicated the mobility of the alkane chains that is helpful for further understanding the diffusion property. (C) 2013 Elsevier Ltd. All rights reserved.