The effect of van der Waals interaction between alkyl chains on the molecular packing density and orientation in the self-assembled monolayers (SAMs) of a series of novel functionalized azobenzene on gold has been studied by reflectance infrared spectroscopy and contact angle measurement. The aromatic interaction between the azobenzene groups and hydrogen bonding between the amide groups help to organize the molecules, forming a well-defined structure. Larger van der Waals interactions introduced by alkyl chains with longer length at the front of the azobenzene group lead to a higher packing density and a larger tilting angle of the molecules.