To determine the distribution of organic selenium in Ornithogalum caudatum Ait. (OC), atomic fluorescence spectrometry was used to detect the content of organic selenium in OC and its polysaccharide. Digestion method was used to deal with the whole grass of OC and its polysaccharides. The selenium content was determined by atomic fluorescence spectrometry. The results indicated that the organic selenium contents of OC whole grass and polysaccharides were 31.471 μg/kg and 56.011 μg/kg. The extraction yield of crude polysaccharides of OC was 25.44%. The selenium content in polysaccharides accounted for 45.22% of OC whole grass. The conclusion can be drawn that AFS method had the advantages of high sensitivity and accuracy, simple operation and low detection limit that is an excellent method for determination of organic selenium content in OC. The OC polysaccharides contained a high amount of organic selenium that accounted for about half of the total selenium in OC.