The invention discloses a method for water-phase microwave preparation of CdSeS quantum dots. The method provided by the invention comprises the following steps of 1, preparing a selenosulfate solution through the reaction of selenium powder and a sodium sulfite solution, 2, weighing cadmium chloride crystals, and carrying out dissolution and volume metering by deionized water to obtain a cadmium chloride solution, 3, adding a certain amount of mercaptopropionic acid into the cadmium chloride solution, 4, adjusting a pH value of the mixed solution obtained by the step 3 to a specific pH value by a sodium hydroxide solution, 5, feeding inert gas into the mixed solution having the specific pH value to remove oxygen, and adding the selenosulfate solution obtained by the step 1 into the oxygen-free mixed solution, 6, loading the mixed solution obtained by the step 5 into a teflon-made digestion tank, and heating for a reaction by a microwave digestion furnace, and 7, cooling the reaction products obtained by the step 6 to a room temperature, adding isopropanol into the cooled reaction products, carrying out purification, and drying by a freezer dryer to obtain solid powder of the CdSeS quantum dots. The method provided by the invention is fast and simple, has easily controllable technological parameters, has a low cost, realizes small sizes and even size distribution of the CdSeS quantum dots obtained by the method, and has a high fluorescent quantum yield. The CdSeS quantum dots obtained by the method can be utilized as a biological fluorescent label material through coupling with biomolecules and can also be utilized for metal ion detection.