Exploring the effects of electron donor (D) and acceptor (A) functional groups in tuning the condensed state properties has been challenging yet efficient approach to reveal promising materials for cutting-edge applications. Herein, a series of boron-nitrogen (BN) incorporated organic congeners (NBNMe2, NBOMe, NBF, NBCl, NBBr, NBCN, NBPy) appended with functional groups having varying degree of D/A characteristics were developed and their potential in controlling supramolecular assembly and condensed state luminescence features (>90 nm redshift in λem.max) were explored. Despite the minor structural engineering in BN-based small molecules, it effectively modulated conformational orientation and molecular packing, leading to the directed growth of distinct and highly ordered self-assembly patterns, i.e., nanosheets, nanospheres, nanowires, and nanorods. The structure-property correlation investigation also highlighted the time-dependent fluorescence enhancement for NBPy owing to morphological growth via the fusion of nanospheres into nanowire conformation. Further, these nano architectures with distinct conformations were employed to examine the mechanistic aspects as well as the influence of morphologies in cellular uptake and imaging, where all the nano aggregates exhibited lysosomal localization following multiple endocytosis pathways and the nanorods possessed the highest uptakes (CTCF4h/0.5h=3.11) with respect to other conformations. The in-depth inspection of the structural impact in single crystal X-ray diffraction (SCXRD) analysis disclosed the decisive role of boron atoms and functional groups tuning, that built a conceptual correlation between the molecular architecture to their photophysical characteristic, supramolecular assembly, and cellular internalization process, offering key insights on the development of rapid and effective drug delivery technique.