Carbon dots (CDs)-induced microstructural modulation and amplification of emission intensity of self-aggregated fluorescent organic nanoparticles (FONPs) is a challenging task since CD is a wellknown fluorescence quencher. In the present study, we have designed tyrosine-tagged hydrophobically (C-10) tailored naphthalene diimide derivative (NDI-i), which formed FONPs in tetrahydrofuran (THF)-water binary solvent mixture. NDI-i exhibited aggregation-induced emission (AIE) at 580 nm (orange) up to f(w) = 70 vol % of water in THF via excimer formation in combination with intramolecular charge transfer (ICT) upon excitation at 350 nm. Beyond f(w) = 70 vol %, the emission intensity gradually reduced up to f(w) = 99 vol % due to poor water dispersibility of NDI-i FONPs. Doping of hydrophobically (C-2 to C-11 alkyl chain) surface-functionalized CDs (CD-i- iii) within self-aggregates of NDI-i FONPs at f(w) = 99 vol % resulted in the modulation of both morphology and emission intensity of resulting self-assembled nanoconjugate. In the presence of C-2 alkyl chain tethered CD, the emission intensity of FONP-CD nanohybrid got quenched compared to that of native NDI-i FONPs. The emission intensity of NDI-i FONPs markedly enhanced by 3.6- to 5.0-fold upon inclusion of C-6 and C-11 alkyl chain containing CDs, respectively. Increasing the alkyl chain length on CD surface facilitated the interchain hydrophobic interaction between the organic nanoparticles and surface-functionalized CDs to form larger CD-doped fused FONPs. The extent of ICT between it-donor and Tr-acceptor residues became more efficient to exhibit enhanced AIE due to the accumulation of more NDI-i around CD surface through interchain hydrophobic interaction. The C-11 alkyl chain containing CD-integrated FONPs showed the brightest orange emission with superior aqueous stability. These water-dispersible, orange-emitting, cytocompatible NDI-i-CD-iii FONPs were explored for long-term bioimaging of mammalian cells.