Abstract: Intestine and gonad of sea cucumber (Apostichopus japonicus) are by-products during its processing process. In order toutilize them better, we analyze the changes in contents of soluble protein and amino acid nitrogen during enzymatic hydrolyzation as well as study their free radical scavenging effects against 1,1-Diphenyl-2-picrylhydrazyl radical (DPPH), hydroxyl free radical (OH) and superoxide anion free radical (O2-) in vitro. Results show that the degree of hydrolysis (DH%) of intestine and gonad after enzymatic hydrolyzation are 53.63% and 63.40% respectively; the contents of soluble protein are 4.62 mgmL-1 and 5.01 mgmL-1, respectively; the contents of amino acid nitrogen are 0.43 mgmL-1 and 0.56 mgmL-1, respectively. The half maximal inhibition concentrations (IC50) of polypeptides prepared from intestine and gonad are 3.31 mgmL-1 and 0.88 mgmL-1 against DPPH, respectively, 9.53 mgmL-1 and 8.81 mgmL-1 against OH, respectively, 6.42 mgmL-1 and 3.22 mgmL-1 against O2-, respectively.The polypeptides from intestine and gonad of sea cucumber have remarkable antioxidation functions with good application prospects.