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The spectroscopic and photophysical properties of organic materials in the films are widely influenced by their molecular packing morphologies and intermolecular interactions. Here, regioisomeric phenanthridine derivatives were synthesized. The UV–vis spectra and scanning electron microscopy images show that these molecules can form different self-organizations in the films. Scanning tunneling microscopy and density functional theory calculations are utilized to reveal their intermolecular interactions by visualizing the molecular packing in the self-assembly adlayers. The different intermolecular Br···N halogen bonds, H···Br hydrogen bonds, and Br···Br type-II halogen bonds are the dominated factors to form the different nanostructures and different morphologies in the films. This work provides a new viewpoint to explore the “molecule-packing-properties” relationship in order to rationally control the properties of organic materials through designing the molecules.