Based on Scanning tunneling microscopy (STM) observations of 1-C18H37X (X = OH, SH) adsorbed on HOPG, the hydrogen bonded complexes were studied using density functional theory (DFT) and molecular mechanics (MM). At, B3LYP/6-31g and B3LYP/6-311g** levels, molecular dimers connected by hydrogen bond were obtained. The models of 1-C18H37X monolayer were optimized by consistent valence force field (CVFF), whose structures and interaction energies agree well with DFT calculations. It is noticed that due to the stronger hydrogen bond interactions between C18H37OH molecules, C18H37OH adsorbed on HOPG shows only one kind of molecular arrangement, while C18H37SH exhibits two kinds of packing induced by alkyl-alkyl and adsorbate-substrate interactions.