The invention relates to a jellyfish bioactive peptide acidophilus milk and a preparation method thereof, which takes high quality jellyfish as raw material and water with the weight of 2 times to 4 times of the weight of the jellyfish is added to the jellyfish which is firstly desalted and mashed to adjust pH value, and then at the temperature of 55 to 60 DEG C, alkali protease is added based on the standard that 800 to 1200 enzyme-activity units (u) are added for each gram of jellyfish before dilution to keep warm for 2 hours to 5 hours for zymohydrolysis, and jellyfish polypeptide liquid with the molecular weight between 1000 daltons to 3000 daltons is prepared after inactivation of enzyme, centrifugal separation and ultrafiltration; and the jellyfish polypeptide liquid, after going through sterilization, is fixed with acidophilus milk prepared in an ordinary method and stirred evenly and aseptic canning is carried out, and then finished products are prepared. The percentage by weight of the jellyfish polypeptide liquid is 5 percent to 20 percent and the percentage by weight of the acidophilus milk is 80 percent to 95 percent. The jellyfish bioactive peptide acidophilus milk is rich in nutrition, easy to absorb, convenient for drinking and good in taste, and has the effects of clearing away heat and toxic material, eliminating sputum and exhausting qi, moistening intestine and eliminating accumulation, realizing angiectasis, reducing blood pressure, and so on. The preparation technology of the invention is reasonable in technology, simple and convenient in preparation and strong in operability, thus being easy in realizing commercial process.