The invention discloses a method for preparing mussel proteins and polypeptide with different dissolubilities. The method comprises the following steps: cleaning, removing shells, removing byssi, and performing homogenization; sequentially extracting myogen, fibrillin and a matrix protein so as to obtain corresponding extracts, performing ultrafiltration respectively, and finally performing spray drying, thereby obtaining protein powder. In addition, the protein extracts are subjected to enzymolysis, enzyme deactivation, centrifugation to obtain supernate, and the supernate is subjected to ultrafiltration and spray drying, thereby obtaining polypeptide powder. According to different dissolubilities, mussel is divided into the myogen, the fibrillin and the matrix protein. By virtue of the characteristics that the myogen is soluble in a water solution or a thin salt solution, the fibrillin is soluble in a salt solution of certain concentration and the matrix protein is insoluble in water, mixed proteins in the mussel are appropriately separated. In addition, the proteins are adopted for enzymolysis respectively, then three different enzymolysis polypeptide products can be prepared, and the utilization rates of raw materials are increased.