Establishing an effective strategy for Hg2+ determination with good sensitivity and high selectivity is of particular concern. In this work, N-doped carbon quantum dots (NCQDs) were obtained for the first time from peels of peach palm fruit (Bactris gasipaes) through microwave-assisted one-pot synthesis. Surface NCQDs was modified with l-cysteine (NCQDs/CYS) by a chemical reaction (known as amide coupling) between the nitrogen-containing groups (amine group) of l-cysteine ligand and the carboxyl groups of NCQDs. The chemical bonding was examined by Fourier Transform Infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). NCQDs/CYS nanoparticles exhibited a quantum yield of fluorescence (ΦFL) of 25.4%, high solubility in water, and a surface with thiol groups from l-cysteine. Mercury ions induced quenching of fluorescence of NCQDs/CYS at low concentrations (Limit of Detection, LOD = 0.19 μM) with great sensitivity. A significant preference for Hg2+ ions was found because of the high affinity between the thiolate groups of NCQDs/CYS and the analyte. Time-resolved fluorescence measurements were done to study the way that led to fluorescence quenching when Hg2+ ions were present, evidencing a static quenching fluorescence mechanism. The new NCQDs/CYS material could be applied to accurately measure the concentration of Hg2+ ions in water samples in a fast and cost-effective way.