In this article, we discuss X-ray fluorescence holography (XFH) using a third-generation synchrotron radiation facility through an application to a DVD-RAM material thin film. Three-dimensional atomic images were obtained at 100 K around the Ge atoms in a Ge2Sb2Te5 single-crystal thin film by means of XFH technique at the beamline BL37XU of the SPring-8 to clarify the high-speed writing and erasing mechanism of this DVD material. From the obtained XFH images, it was concluded that the single-crystal thin film has a mixture of rocksalt and zinc-blende structures. In addition, the images indicate large distortions associated with the existence of vacancies of the Ge(Sb) site. The present XFH results are in good agreement with the previous XAFS results, which has predicted a phase transition due to an umbrella flip motion of the Ge atoms.