The preparation of hypoallergenic ingredients using goat whey protein is a hot research topic in dairy industry. Whey protein is one of the main proteins in milk, and it is also the main substance that causes allergic reactions in infants and young children. The most common way to reduce protein sensitization is to hydrolyze protein into small molecular peptides. The hydrolysis process of partial and extensive hydrolysis, and the characteristics of hydrolysate (degree of hydrolysis, molecular weight distribution and β-Lg antigenicity) were studied with goat whey protein as raw materials. LC-MS/MS was used to compare the cleavage sites of allergic epitopes by partial hydrolysis and extensive hydrolysis. The results showed that neutral protease and alkaline protease hydrolysis had better hydrolysis effect on goat whey protein, in which alkaline protease had the highest hydrolysis degree of 21.26%. Analyzed by electropherograms, macromolecular polypeptide chains still existed in the products after single enzyme hydrolysis, and complex enzyme hydrolysis was required in the extensive hydrolysis process. At the enzyme to substrate ratio of 4000U/g, alkaline protease was used for hydrolysis at pH 10.0 and 55℃ for 1.0h. The degree of hydrolysis of partial hydrolysates was 12.31%, the molecular weight of polypeptides below 5kDa accounted for 95.18%, and the antigenicity of β-lactoglobulin decreased by 9.40%. When the mass ratio of neutral protease and alkaline protease was 1∶1, the enzyme to substrate ratio was 6000U/g, and the hydrolysis was conducted at pH 8.5 and 50℃ for 3.0h, the hydrolysis degree of the extensive hydrolysate was 35.58%, peptides with molecular weight less than 3kDa accounted for 97.26%, and the antigenicity of β-lactoglobulin decreased by 40.97%. Both partial and extensive hydrolysis could destroy most of the allergic epitopes of β-lactoglobulin, but extensive hydrolysis could reduce the allergenicity of whey protein to a greater extent than partial hydrolysis. The purpose of this study was to provide some reference for the production of hydrolyzed whey protein in hypoallergenic goat.