Abstract: Low energy electron diffraction, scanning tunneling microscopy, first－principles density－functional theory, and molecular mechanics calculations were used to analyze the adsorption and growth of quinacridone derivatives (QA) with alkyl chains of 4 and 16 carbon atoms on an Ag(110) substrate. It is found that the alkyl chains determine the orientation of the molecular overlayers, while the interaction of QA and the Ag substrate is primarily due to chemical bonding of oxygen to the silver substrate, which determines the molecular orientation and preferred adsorption site. The intermolecular arrangement can be adjusted by varying the length of alkyl chains, thus uniform QA films may be fabricated with very well controlled physical properties.