Water-soluble Cu nanoclusters (NCs) with tunable emission were synthesized through an eco-friendly one-pot aqueous method. Blue-, green-, and red-emitting NCs with the emission peaks at 420nm, 505nm, and 630nm were obtained by employing ethanediamine, cysteine, and glutathione as surface ligands, respectively. The ligand effects on the optical properties of Cu NCs were studied by the single variable method. It has been revealed by systematic characterizations that the dependence of emission color on the structures of ligands was mainly attributed to their different size-tuning effects. Glutathione has the strongest chelating ability and it can significantly reduce the monomer reactivity and thus decrease the supersaturation degree of the reaction, which is favorable for modulating Cu precursor to grow into larger NCs. In contrast, ethanediamine ligand resulted in smaller nanoclusters due to its weaker binding capability. Because of the strong emission and terrific fluorescent stability, Cu NCs capped with ethanediamine, possessing an emission peak at 420nm when excited at awavelength of 350nm, were directly used for probing Hg(II) with satisfying selectivity, presenting a linear range of 0.1-5.0mM and a detection limit of 33μM. The sensor showed good performance in real sample analysiswith recoveries ranging from 99% to 103%, and comparable accuracy with atomic fluorescence spectroscopy, manifesting the reliability of the current strategy for sensing Hg(II). Graphical abstract Water-soluble copper nanoclusters with blue, green, and red emissions were synthesized by employing ethanediamine, cysteine, and glutathione as surface ligands respectively, and the blue-emitting nanoclusters with strong emission and terrific stability were directly used for selectively sensing Hg2+.