Polymorphism‐dependent cytotoxicity and cellular uptake of drug molecules have been studied for the past two decades. However, visualizing the polymorph‐dependent cellular uptake and cytotoxicity using microscopy imaging technique has not been reported yet. The luminescent polymorph is an ideal candidate to validate the above hypothesis. Herein, we report the polymorph‐dependent cellular uptake, cytotoxicity, and bio‐imaging functions of polymorphs 1Y and 1R of a naphthalimide‐phenothiazine dyad. These polymorphs show different luminescence colors in the solid state and exhibit aggregation‐induced enhanced emission (AIEE) in the DMSO‐Water mixture. Bioimaging, cytotoxicity assay, and fluorescence‐activated cell sorting (FACS) studies revealed that these polymorphs show different levels of cytotoxicity, cellular uptake, localization, and imaging potential. Detailed photophysical, morphological, and biological studies revealed that the difference in molecular conformation in these polymorphs enables them to form aggregates of different sizes and morphology, which leads to the differential uptake of these into the cells and consequently shows different cytotoxicity and imaging potentials.