Knowledge of molecular structures of emerging charge acceptors, such as hexaaza-triphenylene-hexacarbonitrile (HATCN), on metal surfaces is essential for their optoelectronic device applications. Here, we studied the two-dimensional molecular ordering of HATCN at submonolayer coverages on Au(111) using scanning tunneling microscopy (STM). Linear and hexagonal porous structures were observed at atomic steps and terraces, respectively, and our density functional theory calculations revealed that the structures were stabilized with CN···CN dipolar interactions. The hexagonal porous structures possess chirality, and they form only small (<1000 nm2) phase-separated chiral domains that easily change their structures in subsequent STM images at 80 K, which explains the no electron diffraction pattern reported previously.