The chemical bond is of central interest in chemistry, and it is of significance to study the nature of intermolecular bonds in real‐space. Herein, non‐contact atomic force microscopy (nc‐AFM) and low‐temperature scanning tunneling microscopy (LT‐STM) are employed to acquire real‐space atomic information of molecular clusters, i.e., monomer, dimer, trimer, tetramer, formed on Au(111). The formation of the various molecular clusters is due to the diversity of halogen bonds. DFT calculation also suggests the formation of three distinct halogen bonds among the molecular clusters, which originates from the noncovalent interactions of Br‐atoms with the positive potential H‐atoms, neutral potential Br‐atoms, and negative potential N‐atoms, respectively. This work demonstrates the real‐space investigation of the multiple halogen bonds by nc‐AFM/LT‐STM, indicating the potential use of this technique to study other intermolecular bonds and to understand complex supramolecular assemblies at the atomic/sub‐molecular level. A real‐space investigation of the multiple halogen bonds by the non‐contact atomic force microscopy (nc‐AFM)/low‐temperature scanning tunneling microscopy (LT‐STM) technique is demonstrated. Due to the noncovalent interactions of Br‐atom with the H‐atom, Br‐atom and N‐atom, three distinct types of halogen bonds form and are investigated in real‐space. This work suggests AFM/STM as a powerful technique to study the nature of intermolecular bonds at the sub‐molecular level.