This invention discloses manufacture of water-soluble ZnSe/ZnS core/shell quantum dots by photodegradation together with program-controlled microwave radiation method. The method comprises the steps of: mixing zinc salt or zinc oxide with water-soluble thioglycollic acid in water phase, adding sodium selenium sulfite or potassium selenium sulfite formed by reaction of sodium sulfite or potassium sulfite with selenium powders, reacting to obtain ZnSe precursor solution, placing the solution in a glass tube for microwave radiation, controlling the microwave radiation by program to obtain ZnSe quantum dots, performing photodegradation to obtain water-soluble ZnSe/Zns core/shell quantum dots with a high fluorescence quantum efficiency. The method is completely operated in water phase, thus has such advantages as easy operation and low toxicity. The quantum dots manufactured have such advantages as high fluorescence quantum efficiency, high stability and good water solubility, and can be used as fluorescent labels and indicators for biological inspection and analysis.