The use of biomass feedstocks for producing high-value-added chemicals is gaining significant attention in the academic community. In this study, near-infrared carbon dots (NIR-CDs) with antimicrobial and bioimaging functions were prepared from Epigynum auritum branches and leaves using a novel green synthesis approach. The spectral properties of the synthesized NIR-CDs were characterized by ultraviolet–visible (UV-Vis) absorption and fluorescence spectroscopy. The crystal structures of the NIR-CDs were further characterized by high-resolution transmission electron microscopy (HR-TEM), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (NMR), and X-ray diffraction (XRD). The NIR-CDs exhibited minimal toxicity, excellent biocompatibility, and high penetrability in both in vivo and in vitro environments, making them ideal luminescent probes for bioimaging applications. Moreover, the antimicrobial activity of NIR-CDs was tested against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli), showing significant bacterial growth inhibition. The antimicrobial effect is likely attributed to the NIR-CDs disrupting the cell membrane integrity, leading to the leakage of the intracellular contents. Therefore, NIR-CDs hold promise as fluorescent bioimaging probes and antimicrobial agents.