Bio-imaging is a crucial tool for researchers in the fields of cell biology and developmental biomedical sector. Among the various available imaging techniques, fluorescence based imaging stands out due to its high sensitivity and specificity. However, traditional fluorescent materials used in biological imaging often suffer from issues such as photostability and biocompatibility. Moreover, plant tissues contain compounds that cause autofluorescence and light scattering, which can hinder fluorescence microscopy effectiveness. This study explores the development of fluorescent carbon dots (Cm-CDs) synthesized from Citrus medica fruit extract for the fluorescence imaging of Vigna radiata root cells. The successful synthesis of CDs with an average size of 6.7 nm is confirmed by Transmission Electron Microscopy (TEM). The X-ray diffraction (XRD) analysis and raman spectroscopy indicated that the obtained CDs are amorphous in nature. The presence of various functional groups on the surface of CDs were identified by Fourier transform infrared (FTIR) spectra. The optical characteristics of Cm-CDs were studied by UV-Visible spectroscopy and photoluminescence spectroscopy. Cm-CDs demonstrated strong excitation-dependent fluorescence, good solubility, and effective penetration in to the Vigna radiata root cells with multicolor luminescence, and addressed autofluorescence issues. Additionally, a comparative analysis determined the optimal concentration for high-resolution, multi-color root cell imaging, with Cm-CD2 (2.5 mg/ml) exhibiting the highest photoluminescence (PL) intensity. These findings highlight the potential of Cm-CDs in enhancing direct endocytosis and overcoming autofluorescence in plant cell imaging, offering promising advancements for cell biology research.