Abstract: To realize the comprehensive utilization of corn residue, the corn residue of starch syrup by-product with extrusion technology was hydrolyzed by the Alkaline Protease 2709. Gel column filtration chromatography and automatic amino acide analyzer were used to determine the molecular distribution, amino acid compositions and contents in the hydrolysate. The results showed that protein in by-product can better be hydrolyzed by the Alkaline Protease 2709, the products with molecular weight(Mw) below 1000 u in hydrolysate was over 94.8%, and most of hydrolysate are dipeptides or tripeptides. The enzyme hydrolysate contains many amino acids necessary for human being.