The invention discloses a method for preparing an antioxidative peptide from skipjack processing by-products. The method comprises the following steps of mixing head sections and tail sections as by-products rich in proteins and a stewing liquor, crushing the mixture, carrying out synchronous three-phase separation to obtain a protein source which can be subjected to direct enzymolysis, adding a flavourzyme into the protein source, carrying out enzymolysis at a pH value of 6.5 at a temperature of 50 DEG C for 4h, purifying the enzymatic hydrolysate by ultrafiltration, activated carbon adsorption and desalination, and carrying out spray drying to obtain peptide powder. Various antioxidant activities of the peptide powder are detected. The peptide powder has good DPPH free radical, superoxide anion free radical and hydroxyl radical removal rates, has IC50 of 3.55mg/ml, 1.39mg/ml and 0.61mg/ml and is an excellent anti-oxidant. The peptide powder is flavescent, has no bitter taste, has a light fishiness taste, has molecular weight (greater than 90.1%) less than or equal to 10000Da, has polypeptide total protein content of 88.6% by dry weight and has ash content of 7.2%.