Uniform and well-defined interfaces are required for clarification of fundamental processes at internal interfaces between donor and acceptor molecules constituting organic optoelectronic devices. In this study, evolution of a well-ordered molecular interface, epitaxially grown C60 on the single crystal rubrene (C42H28) surface, was accurately investigated by grazing incidence x-ray diffraction (GIXD) techniques. Contrasting to the case of C60 on the single crystal pentacene forming uniquely aligned epitaxial interfaces, coexistence of two inequivalent crystalline domains of C60 was identified on the single crystal rubrene. Nevertheless, crystallinity of C60/rubrene exhibited even more remarkable improvement to extend its in-plane average crystallite size up to 250 nm as the growth temperature was raised. Probable leading factors determining the structures and crystallinity of the well-defined molecular interfaces are discussed based on close comparison of the present results with the C60/pentacene interfaces. The techniques presented herein for enhancement of the crystallinity in epitaxial molecular interfaces are potentially applicable to development in the photoelectric power conversion efficiency of organic photovoltaics (OPVs) via improved charge carrier mobility in donor-acceptor interfaces.