The invention relates to a method and a kit for labeling the karyon stably by fluorescence, in particular to a method which carries out fluorescent labeling to the karyon by combining semiconductor nano-material quanta dots with organic fluorescent dye DAPI or PI, and a kit which contents the quanta dots and the DAPI or PI and is used for stable fluorescent labeling of the karyon. The method and the kit can label the karyon by fluorescence simply, effectively and stably, provide a testing method of karyon stable tracking for the long-term investigation and research of the cell and can be usedfor long-term tracking of cells or tissues and the like.