The invention discloses a sea cucumber polypeptide functional food and a preparation method thereof which not only remarkably improves the content of polypeptide, but also has no chemical residues; the contents of salt and arsenic are low; the food is healthier and safer to eat; simultaneously the food is simply operated, easily controlled, is effective and saves energies. The key technical scheme includes: selecting a compound protease of Protamex and needing not to adjust the pH value of materials; carrying out processes of desalting and arsenic removing on an enzymolysis liquid; more than 80 percent of the molecular weight of the product is between 100 to 6000Dalt; wherein, the small polypeptide of 100 to 2100Dalt is more than 70 percent; the product components and the content weight percentages are as follows: 50 to 60 percent of polypeptide, 5 to 10 percent of free amino acids, 2.5 to 7.5 percent of mucoitin as well as containing the inherent nutrition components of a plurality of minerals and vitamins of the sea cucumber. The product has the effects of resisting knub, reducing blood pressure, preventing cardio-cerebrovascular diseases, resisting fatigue, delaying senescence, improving the immunity. The food can be used as a healthy food to eat and can also be used as a food and a medicine additive.