The oriented crystallization of caffeine and theobromine on self-assembled monolayers (SAMs) is reported. The SAMs were prepared by reacting 1-decanethiol, 11-mercapto-1-undecanol, or 11-mercaptoundecanoic acid on flat Au surfaces to form methyl, hydroxyl, or carboxylic acid functionalities on the substrates. Crystallization was conducted by sublimating the xanthine alkaloids on the SAMs. X-ray diffraction and morphology observation/simulation were combined to identify the preferred orientation of caffeine and theobromine crystals. Also, the identified crystal orientation was examined through molecular models to understand the nature of the interfacial interactions that direct the nucleation process. CH/π interaction as well as strong hydrogen bonding appeared to act as the specific interactions to control the molecular orientation of caffeine and theobromine in stereochemically determined manners that persisted during the crystallization process. More importantly, the stability of the orientational regulation showed a clear correlation to the cohesiveness of the xanthine molecular layer parallel to the nucleating substrate. We believe this indicates that the structural coherence of the precursors or nuclei of the crystallization is essential to effectively utilize the interfacial interactions in a cooperative manner to firmly control the crystal orientation.