Abstract: The Microcoleus vaginatus was screened from the desert soil, the intracellular polysaccharides(IPS) and exopolysaccharide(EPS) were obtained via water extraction and ethanol precipitation method, the extraction rate, yield rate and antioxidant activity were determined respectively. The results proved that the highest extraction rates of intracellular polysaccharide and exopolysaccharide were 3.46% and 77.98% respectively, the highest yield rates of intracellular polysaccharide and exopolysaccharide were 83.67% and 50.76%, respectively. Protein content measured by Coomassie brilliant blue staining method was as low as 3.26%. The polysaccharides can effectively remove the superoxide anion radical, DPPH free radical and hydroxyl radical and weakly chelate ferrous ions in vitro. The analysis of Fourier infrared spectroscopy showed that the hydrogen bonding between molecules were prevalent in the M. vaginatus polysaccharides, and the monosaccharides were present in the form of pyranoside, and the glycosidic bond is α-type.