The invention discloses an industrial manufacturing method and a use of CPPs-containing hypoallergenic casein peptide whole-powder and belongs to the field of food biotechnology. Food-grade casein as a raw material is subjected to two-step enzymolysis by more than eight compound enzymes dividing into two groups so that the CPPs-containing hypoallergenic casein peptide whole-powder is obtained. The CPPs-containing hypoallergenic casein peptide whole-powder has CPPs content more than 15%, has 90% of molecular weight less than 5000Da, reduces protein antigenicity by more than 60% than protein antigenicity before hydrolysis, reduces allergen alpha s1-casein content by more than 95% than before and belongs to a hypoallergenic food. The industrial manufacturing method has a high yield, a low processing cost and a large processing amount and is convenient for industrial production. The CPPs-containing hypoallergenic casein peptide whole-powder has high CPPs content, a moderate protein hydrolysis degree and a small bitter taste, can be digested and absorbed easily, eliminates most sensitization activity and can be widely used in fields of common foods, adult milk powder, infant formula foods, movement nutrition foods, health foods and drugs.