On the basis of ab initio molecular dynamics simulations, large voids mainly surrounded by Te atoms are observed in molten and amorphous Ge2Sb2Te5, which is due to the clustering of two- and threefold coordinated Te atoms. Furthermore, pressure shows a significant effect on the clustering of the under coordinated Te atoms and hence the formation of large voids. The present results demonstrate that both vacancies and Te play an important role in the fast reversible phase transition process.