A simple and effective quantum dots (QDs)-based sensing method for copper ion (Cu(2+)) in water is developed with improved selectivity and ultrahigh sensitivity in the presence of thiosulfate. For this, hexadecyl trimethylammonium bromide (CTAB) modified CdSe/ZnS QDs is used as a fluorescent probe. In the absence of thiosulfate, mercury and silver ions show strong interference with Cu(2+) ions even though the sensitivity can be obtained within a few nanomolar. By using our method, the lowest detected concentration for Cu(2+) is 0.15 nM in the presence of thiosulfate in DI water. Also, it is successfully demonstrated for Cu(2+) ion detection in practical application (tap water) down to lowest detection limit, 0.14 nM. This method provides a good potential for copper ions detection with simplicity, rapidity, ultrahigh sensitivity, and excellent selectivity.