The development of stimuli-responsive molecular electronic devices relies on a comprehensive understanding of the nature and strength of interactions that govern their self-assembly on solid surfaces. Here, we report spatially resolved two-dimensional self-assemblies of fluorinated azobenzene derivatives using scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite substrate. STM images show that fluorine-substituted azobenzene derivatives form large-scale monolayers stabilized by intermolecular hydrogen and halogen bonding, unlike their nonfluorinated counterparts. Incorporating an alkoxy chain into the molecule changes the balance of molecule−molecule and molecule−substrate interactions by introducing stronger molecule−substrate coupling due to van der Waals interactions. High-resolution STM images enable us to observe alkylation-induced changes in the atom-specific intermolecular interactions among polar atoms F, O, and N in the azobenzene cores of the molecules. Our results clearly highlight the significance of minor chemical modifications such as fluorination and alkylation in adjusting the intermolecular and molecule−substrate interactions to achieve precise molecular packing on solid supports.