Chlorophyll-derived carbon dots (CDs) with strong deep red emission is an ideal candidate for high-quality bio-imaging in the NIR window. However, its low aqueous dispersity with severe emission quenching has limited its biological application. Herein, chlorophyll-derived CDs from mulberry leaf (MCDs) have been successfully coated with polyethylenimine (PEI) via a simple and mild solution-mixing method at room temperature. Experimental optimization proved that the MCDs produced at a reaction temperature of 120 °C and a reaction time of 4 h had the best PL strength, while the PEI-MCDs produced at a PEI/CDs ratio of 0.4 ‰ had the best PL strength. The PEI-MCDs composites demonstrate good aqueous dispersity and exceptional fluorescence stability under various conditions like UV irradiation, temperature fluctuations, salt and various substances. A strong narrow-band deep-red emission at 670 nm with quantum yield (QY) of 45.44 % is obtained in PEI-MCDs aqueous solution. The mechanism of lipophilic-hydrophilic transformation and emission recovery in aqueous solution is confirmed to be the amphiphilicity shell of PEI on MCDs, which effectively improves the aqueous dispersity and suppresses the occurrence of aggregation-caused quenching. Selective imaging of lysosomes in various cells has been realized by utilized PEI-MCDs without targeting ligands. Furthermore, clear tissue structures were shown in the in vivo fluorescence imaging of zebrafish embryos and larvae. The results indicate PEI-MCDs own notable amphiphilicity, superior stability and excellent deep-red emission, which hold great promise for biological imaging applications.