The adsorption and self-organization of trans-azobenzene (TAB) on Ag/Ge(111)-(3×3)R30° (Ag/Ge(111)-3) were studied by low temperature scanning tunneling microscopy (LT-STM) in ultrahigh vacuum (UHV). High-resolution STM images allow the observation of individual TAB molecules and the commensurate TAB chain domains formed via the hydrogen bond enhanced intermolecular interaction and molecule–substrate interaction on Ag/Ge(111)-3. From in situ observation of the substrate lattice, the TAB monolayers were found to form a (2×1) structure. Some coexisting cis-azobenzene (CAB) molecules were observed on the domain boundary of TAB overlayer. The structural model and the molecule registry corresponding to STM images for the monolayer of TAB on Ag/Ge(111)-3 are proposed and discussed.