A novel approach to producing core/shell quantum dots（QDs） of ZnS∶Mn/ZnS was developed by nucleation doping strategy using thioglycolic acid（TGA） as stabilizer. The producing mechanisms of fluorescence and room temperature phosphorescence（RTP） were studied. The fluorescence,RTP analysis methods were developed for the determination of DNA with functionalized water soluble ZnS∶Mn/ZnS QDs as a labeled probe,based on the fluorescence,RTP enhancing of the QDs in the presence of DNA,respectively. The influences of experimental conditions,such as concentration of QDs,amount of EDC/NHS and reaction time,were investigated. The results showed that,under the optimal conditions,the calibration curves of both the methods were linear in the range of 50-600 μg/L for ctDNA. The detection limits for the fluorescence and RTP method were 39.6,28.5 μg/L,respectively. The recoveries were in the range of 98%-104% and 99%-101% with relative standard deviations（n=25） for 300 μg/L ctDNA of 3.1% and 2.3%,respectively. The methods were simple,safe and sensitive for the determination of trace DNA.