The state of organic surfaces/interfaces greatly affects the performance of organic electronic devices. Various methods have been reported to investigate the surface glass transition temperature, which is based on the dynamics of molecules or polymer chains existing at the depth of several to several-tens nanometers from surface. However, no report has published about the characterization of molecular kinetics on the outermost surface. We report that the surface nucleation of Mg-vapor atoms reflects the molecular kinetics on the outermost surface. The nucleation rate of vaporized atoms/molecules is generally accelerated on steps existed on crystalline surface, to the contrary we found suppressed nucleation of Mg nanocrystals around the steps on a diarylethene crystalline surface during Mg-vapor deposition. On the other hand, Pb, Bi, and Te nanocrystals tended to accumulate the steps. The difference between acceleration and suppression of metal nucleation on the steps was attributed to molecular kinetics on the outermost surface and intensity of van der Waals interaction between metal atoms and the molecules. Mg having the weak interaction with organic molecules is suitable for characterizing molecular kinetics on the outermost surface. The observation of Mg nucleation can play a role in measuring molecular kinetics on the outermost surfaces.