The invention discloses a method for preparing coconut polypeptides. The method includes steps of firstly, preparing coconut proteins; secondly, uniformly mixing the coconut proteins and distilled water with one another and carrying out heating and pressure treatment to obtain moist and hot coconut protein serous fluid; thirdly, regulating the pH (potential of hydrogen) of the moist and hot coconut protein serous fluid, adding primary complex enzymes into the moist and hot coconut protein serous fluid and carrying out ultrasonic-assisted enzymatic hydrolysis to obtain primary enzymatic hydrolysate after primary enzymatic hydrolysis reaction is completely carried out; fourthly, regulating the pH of the primary enzymatic hydrolysate, adding secondary complex enzymes into the primary enzymatic hydrolysate, and carrying out ultrasonic-assisted enzymatic hydrolysis to obtain secondary enzymatic hydrolysate after secondary enzymatic hydrolysis reaction is completely carried out; fifthly, carrying out microwave enzyme deactivation treatment on the secondary enzymatic hydrolysate to obtain enzyme-deactivated enzymatic hydrolysate, sequentially cooling and centrifuging the enzyme-deactivated enzymatic hydrolysate to obtain supernatant, carrying out ultra-filtration to obtain filter liquor and carrying out freeze drying to obtain the coconut polypeptides which are finished products. The method for preparing the coconut polypeptides has the advantages that the method includes safe processes, and the coconut polypeptides can be conveniently and quickly prepared by the aid of the method and are high in purity.