Construction of tunable and robust two-dimensional (2D) molecular arrays with desirable lattices and functionalities over a macroscopic scale relies on spontaneous and reversible noncovalent interactions between suitable molecules as building blocks. Halogen bonding, with active tunability of direction, strength, and length, is ideal for tailoring supramolecular structures. Herein, by combining low-temperature scanning tunneling microscopy and systematic first-principles calculations, we demonstrate novel halogen bonding involving single halogen atoms and phase engineering in 2D molecular self-assembly. On the Au(111) surface, we observed catalyzed dehalogenation of hexabromobenzene (HBB) molecules, during which negatively charged bromine adatoms (Br delta-) were generated and participated in assembly via unique C-Br delta+center dot center dot center dot Br delta- interaction, drastically different from HBB assembly on a chemically inert graphene substrate. We successfully mapped out different phases of the assembled superstructure, including densely packed hexagonal, tetragonal, dimer chain, and expanded hexagonal lattices at room temperature, 60 degrees C, 90 degrees C, and 110 degrees C, respectively, and the critical role of Br delta- in regulating lattice characteristics was highlighted. Our results show promise for manipulating the interplay between noncovalent interactions and catalytic reactions for future development of molecular nanoelectronics and 2D crystal engineering.