Computational studies including geometry optimizations and molecular dynamics (MD) simulations are carried out for self-assembled monolayers of n-alkanethiols (RSH, R = C16H33, C17H35) and 4＇-alkoxybiphenyl-4-thiols (ROC12H8SH, R = C16H33, C17H35) on the (111) surface of gold with a full atomic representation force field. In this work, we combine the information derived from scanning tunneling microscopy (STM), surface reflection infrared spectra (IR), and computational studies to uncover the origins of different odd-even effects observed by IR for long chain n-alkanethiols and 4＇-alkoxybiphenyl-4-thiols and then to establish a relationship between chemical structures of the headgroups and packing structures of thiols on Au(111). Computationally, the odd-even effect is monitored by the relative magnitude of z-components (the direction normal to the Au surface) of the methyl group. Although both n-alkanethiols and 4＇-alkoxybiphenyl-4-thiols occupy the same spacing on Au(111), according to our simulation results, their favored packing structures are different. Because the headgroup of 4＇-alkoxybiphenyl-4-thiol (-SC12H8O-) is more rigid than that of n-alkanethiol (-S-), 4＇-alkoxybiphenyl-4-thiol prefers more structured packing arrangements and thus its odd-even effect is stronger than that of n-alkanethiol. In other words, the flexibility of the headgroup greatly influences the variety of possible packing structures. Finally, with this new relationship, we are able to rationalize the strong odd-even effect of a new SAM molecule, n-alkyldithioic acid, on Au(111).