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The ability to tune optical features of BODIPY materials is essential for their photo-related application. However, it is challenging to efficiently tune the crystal packing of BODIPY derivatives because of their complex nature. In this study, such control of BODIPY supramolecular assemblies was achieved by designing a BODIPY containing a halogen bond (XB) acceptor (–NO2) and donor (I, Br) to mediate halogen bonding interactions. The mono halogenated 2 and 4 was unable to form XB, whereas 3 and 5 formed isostructural mono-coordinate motif 3, 5-I (1D tubular structure) and symmetric bifurcated motif 5-II (1D zig-zag chains structure) via N-O···I,Br XB interactions. The results show that the dispersion and electrostatic component are the major source of 3, 5-I and 5-II XB formations. The XB interaction between –NO2 and X (I, Br) promote singlet-to-triplet intersystem crossing and triplet-to-singlet reverse intersystem crossing due to delocalization of oxygen electrons partially onto the Br and I. Then this interaction leads to unexpected fluorescence enhancement of 5-II. Finally, the indirect optical band gaps of the 3, 5-I and 5-II were able to be tuned in the range of 1.9–2.50 eV via XB driven crystal packings.