Belonging to the field of biotechnologies, the invention relates to a preparation method of a corn oligopeptide. The method comprises: taking corn protein powder as the raw material, conducting a pretreatment by a continuous countercurrent ultrasonic technology, extracting yellow pigment, carrying out enzymolysis on the well treated raw material by an enzyme membrane reactor, collecting peptide fragments with a proper molecular weight, and performing concentrating and belt vacuum drying, thus obtaining the corn oligopeptide prepared with a lot of physiologically active functions. While preparing the corn oligopeptide, the corn oligopeptide preparation method disclosed in the invention also makes use of the continuous countercurrent ultrasonic extraction technology to extract corn yellow pigment. The process is simple, at the same time, the solvent consumption is reduced to an amount accounting for 40%-50% of that of traditional extraction methods, and the yield is increased by 20%-40%. By using the enzyme membrane reactor to perform enzymolysis on the protein powder, the controllability is good, the prepared corn oligopeptide has a concentrated molecular weight and purity improved by 10%-20%, and has the physiological function activities of hangover alleviating, liver protection, immunoregulation and the like.