In this research we distinguish the live cells,dead cells and other large particles accurately in the UHT milk samples using a new Fluorescence Labeling Technique basing on single live cell,and quickly detect microorganism quantitatively by using flow cytometry.Comparison with traditional plate counting method shows that the detection range of FCM is 101~107 CFU/mL,far above that of plate counting method.Correlation analysis of the results of the two methods shows that within certain concentration range of bacteria solution,the results of FCM and plate counting method are linear,and FCM is a more accurate and rapid detection method for different types of microorganism.