Abstract: Synchrotron radiation X-ray fluorescence spectroscopy is an analytical method used to obtain the composition of material. Compared with the ordinary X-ray fluorescence spectrum, the synchrotron radiation X-ray fluorescence spectrum has the advantages of high radiation intensity, high straightness, short spectrum acquisition time, and small light spot. Synchrotron radiation X-ray fluorescence can be used to analyze gemstone samples by mapping or line scanning conveniently. In this paper, four agate samples from Alashan were tested by synchrotron radiation X-ray fluorescence to introduce the advantage of this technique. According to the characteristics of the samples, two samples were tested by mapping and two samples were tested by line scanning. The element distribution graph of agate samples was obtained by mapping or line scanning, which reflected the difference of the element relative content in different colour areas. The result shows that the red mineral and yellow colour in agate are related to Fe, in this area, the relative content of Fe is much higher than other area. Raman spectrometer were used to determine the red mineral in sample CM-2, which shows that the red mineral are hematite. The yellow colour of the agate may be caused by fine goethite combined with previous studies.