Amphiphilic azobenzene molecules offer ample scope to design functional supramolecular systems in an aqueous medium that can be controlled by light. Despite their widespread applications in photopharmacology and optoelectronics, the self-assembly pathways and energy landscapes of these systems are not well understood. Here, we report combined molecular dynamics (MD) simulation and surface manometry studies on a specially designed alkylated, meta-substituted azobenzene derivative to quantify the hydrogen-bonding interactions in the self-assembled monolayers of its photoisomers. The z-density profile, radial distribution function, order parameters, and hydrogen bond analyzed using MD simulations corroborated the experimental observations of changes in surface pressure, dipole moment, and thickness of the monolayers. Even a small change in the number of hydrogen bonds in the molecule-molecule and molecule-water interactions causes significant changes in the monolayer properties. These results are fundamentally important for engineering photoresponsive molecules with tailored properties for applications in targeted drug delivery and other industrial applications.