A set of 1,8-naphthalimide (NPI)-substituted 4,4-difluoroboradiaza-s-indacene (BODIPY) dyads 1 a-1 c were designed and synthesized by the Pd-catalyzed Sonogashira cross-coupling reaction of ethynyl substituted NPI 1 with the meso-, β-, and α-halogenated BODIPYs a, b, and c, respectively. The BODIPY 1 c exhibits redshifted absorption, which suggests better electronic communication with substitution at the α-position of BODIPY compared with at the meso and β positions, which was further supported by time-dependent DFT calculations. The optical band gap follows the order 1 a>1 b>1 c. The single-crystal X-ray structures of dyads 1 a-1 c are reported, which reflect planar orientations of the BODIPY units with respect to the NPIs. The DFT-optimized structures show good correlation with the experimental data obtained from the single-crystal X-ray structures. The packing diagram of 1 a shows a sheet-like arrangement, 1 b forms a ladder-like structural motif, and 1 c forms a complex 3D structural arrangement. The dyads 1 a-1 c show low cytotoxicity (IC >100 μm). The confocal microscopy studies with HeLa and A375 cells (when treated with dyads 1 a-1 c) show that all the dyads easily enter the cell membrane and show significant multicolor intracellular fluorescence covering the entire visible range with clear emissions in blue, green, and red channels.