The invention discloses a method for producing sea cucumber polypeptide, and belongs to the technical field of food deep processing. The method comprises the steps of preparing the sea cucumber polypeptide by a microbial fermentation method using a sea cucumber intestine as a raw material. The microbial fermentation method specifically comprises the steps of adding a microbial culture solution tothe sea cucumber intestine for treatment, wherein a selected microorganism is Bacillus natto derived from the China Center of Industrial Culture Collection and with a strain number of CICC 10023. Themethod of the invention makes sea cucumber processing sub-products, the sea cucumber intestines, become treasure from waste, the process is simple and the cost is low, and at the same time, pollutioncan be effectively reduced, and the technical scheme of the invention can generate huge economic and social benefits, and thus has good practical application value and broad industrial application prospects.