The combination of organic dyes as photosensitizers with inorganic upconversion nanoparticles (UCNPs) has significantly enhanced upconversion luminescence when excited with near-infrared (NIR) light. Additionally, by employing surface functionalization techniques, a high signal-to-noise ratio can be achieved, resulting in exceptional resolution for bioimaging. The objective of our study was to develop a heptamethylcyanine derivative (IR61-BF) for dye-sensitized UCNPs, enhancing their luminescence efficiency in aqueous solutions. This was done by introducing a difluorobenzene group into the cyanine structure. Rare earth-doped UCNPs with a core–shell structure, NaYF4:YbTm@NaYF4:YbNd, were synthesized using a high-temperature decomposition method. In this structure, the Nd3+ ions function as efficient sensitizers by absorbing 808 nm NIR light. To further enhance the upconversion efficiency, the molecular structure of the NIR dye IR61 was optimized. By integrating a difluorinated phenyl group into the cyanine backbone, we significantly increased the fluorescence quantum yield of the dye and enhanced the dye sensitization effect of the UCNPs. Subsequently, the UCNPs were coated with an amphiphilic ligand, DSPE-PEG, and IR61-BF was incorporated into the hydrophobic region between the UCNPs, and a remarkable 167.1-fold enhancement in upconversion luminescence in the aqueous phase was achieved. Their biocompatibility for neuronal imaging was evaluated using NSC34, Neuro2a, and C6 glioma cells, while their potential for retrograde intra-neuronal delivery was confirmed by using a microfluidic model of cortical neurons. We demonstrated that the newly synthesized heptamethine cyanine derivative IR61-BF shows exceptional sensitization of UCNPs due to the incorporation of a difluorobenzene group, particularly in aqueous solutions.