Characterization of surface and thin films is one of the most essential fields in the research and development of functional materials. Recently, we developed a new X-ray diffraction system, namely an energy dispersive-total reflection Xray diffraction (ED-TXRD) for the surface and thin film studies. In order to demonstrate the capabilities of this system for the structural and orientational characterizations of thin films, organic thin films (perfluoro-n-alkane, n-alkane) vacuum-evaporated on alkali halide single crystals were evaluated by the ED-TXRD system. Moreover, the potential calculation was conducted based on van der Waals interaction between thin films and substrate, and the most energetically preferable molecular arrangement was estimated by the simulation. The epitaxial growth of the long chain molecules are especially discussed in detail through their experimental and theoretical results.