The invention discloses a submerged fermentation phellinus linteus mycelium glycoprotein, a usage and a separation extraction preparation method thereof, the complex is the complex of heteropolysaccharide and protein, wherein, the content of the heteropolysaccharide is 15 to 20 percent, and the heteropolysaccharide is composed of three monosaccharides of glucose monosaccharide, xylose and mannose; the content of the protein is 80 to 85 percent, and the protein is composed of 18 amino acids of aspartic acid, glutamic acid, arginine and so on; and the weight-average molecular weight is 20 to 40KD. The glycoprotein complex uses bran extract liquid as a main ingredient for preparing a culture medium, the phellinus linteus mycelium is produced by the submerged fermentation of the phellinus linteus bacterial strain liquid, the homogenization, the cold-water extraction, the centrifugalization, the collection of supernatant liquid, the precipitation of ammonium sulfate, the dialysis and the DEAE-Sepharose Fast Flow column chromatography are carried out for system separating and purifying the glycoprotein complex. The anti-bacterial glycoprotein is used for preparing the anti-bacterial dugs which have inhibitory effects on escherichia coil and staphylococcus aureus. At the same time, the glycoprotein complex can be used for the separation and the purification of the glycoprotein from the mycelium obtained by the submerged fermentation of various medical and edible fungi.