Recently developed ultrathin two-dimensional (2D) organic semiconductor crystals are a promising platform for advanced organic electronic devices. Remarkable quality of such crystals results in charge-carrier mobilities comparable to those of bulk crystals, but their structure and orientation are hard to study because of their extremely small thickness. Here, we applied surface-enhanced Raman spectroscopy (SERS) to investigate the structure of the thinnest 2D single crystals—monolayers, which are based on thiophene-phenylene co-oligomers: 1,4-bis(5′-decyl-2,2′-bithiene-5-yl)benzene and 1,4-bis(5′-hexyl-2,2′-bithiene-5-yl)benzene. Their Raman spectra were calculated as a function of the molecule orientation and SERS microscopy maps were acquired. High sensitivity of SERS allowed us to study monolayer single-crystal domains with the optical spatial resolution. Raman anisotropy was used to probe the orientations of single-crystal domains and the molecule orientation within them. Notably, the SERS microscopy detected the presence of a submonolayer—amorphous material between the crystalline domains, which is practically inaccessible to optical or conventional atomic force microscopies (AFMs). The submonolayer was also studied by lateral-force AFM, which showed notably higher friction and adhesion. We found that the measured Raman anisotropy significantly reduced by the metal-covered substrate still allowing us to distinguish orientations of molecules in the 2D crystals and in the submonolayer. Anisotropy-sensitive SERS was shown to be promising for studying 2D organic semiconductor crystals.