The structures of long-chain alkanethiols (C₁₈H₃₇SH) chemisorbed on an Au(111) single crystal were investigated using reflection high-energy electron diffraction (RHEED). The primary structure observed as a major species in the as-deposited films contains gold adatoms below the sulfur headgroups. Between the small ordered domains with the alkyl chains tilting toward six directions are azimuthally disorderly packed regions, with a similar average tilt of 30.2°. In contrast, a significant reduction in the coverage of gold adatoms is found in the thermally-induced phase. This superlattice is shown to contain a mixture of two sulfur arrangements, both of which exhibit a small S–S distance, and the pairing of the aliphatic chains. A microscopic picture is then given for the structural transition. These findings demonstrate how the RHEED technique may be used to resolve structures of nanometer-thick thin films with multiple orders at the interfaces.