In this article, we have designed L-aspartic acid-linked naphthalene diimide (NDI)-based amphiphilic molecules having a benzyl ester group at both the terminals with varying substituents (NAB-1-5). The substituent was judiciously modified from an electron-withdrawing group (EWG) like nitrobenzene to an electron-donating group (EDG), methoxybenzene, and finally to an extended aromatic residue (naphthalene) to regulate the p-electron density at the terminal of NDI derivatives. All of the synthesized NDI derivatives were molecularly dissolved in dimethyl sulfoxide (DMSO), and with an increase in the water content within the DMSO solution, the NDI derivative starts to get self-assembled through J-aggregation at and above 40% water content. Self-assembled spherical organic nanoparticles formed in 99% water in DMSO (f(w) = 99%) were characterized by microscopic studies. All of the NDI derivatives showed very weak emission in the molecularly dissolved state (DMSO). Aggregation-induced emission (AIE) was observed for the NDI derivatives (except NAB-1) at the self-assembled state through excimer formation. Upon excitation at 350 nm, the emission maxima of these NDI-based AIE luminogens (AIE-gens) (NAB-2-5) get red shifted from 463 to 588 nm upon altering the substitution from EWG to EDG at the donor site. Inclusion of proper donor-acceptor moieties in the molecular backbone of the self-assembling unit can govern the AIE in combination with the intramolecular charge-transfer process. Consequently, the emission color of these AIE-gens (NAB-2-5) gets tuned from cyan blue to faint green to strong green and finally to bright orange. The tunable aggregation-induced multicolor emission was investigated by different spectroscopic techniques. These cytocompatible, multicolor-emitting fluorescent organic nanoparticles were utilized for bioimaging applications.