A method for preparing powder rich in whey small peptides with molecular weight of 1000 daltons belongs to the technical field of processing dairy products. The main production process thereof is as follows: enzymatic hydrolysis, embedding and homogenization are firstly carried out on concentrated powder (WPC80 powder) containing 80 percent of whey protein, then the powder is prepared by spray drying, and the product can be used as functional ingredients for infant milk powder. The method adopts trypsin for enzymatic hydrolysis, the degree of hydrolysis achieves 20-21 percent, and then hydrophilic-hydrophobic wall materials of 5-10 percent of beta-cyclodextrin and 5-8 percent of lecithin are adopted, so the method can not only bury the bitterness, but also maintain the biological activities of anti-protein allergy and improve the immunity of the whey small peptides with the molecular weight of 1000 daltons to the maximum extent. The method can be applied to the infant formula milk powder and have good effects of improving the ability of anti-protein allergy of the infant milk powder and improving the immunity.