The effects of Alcalase (AT), Protamex (PT) or Flavorzyme (FT) treatment on the antigenicity and molecular mass distribution of proteins, flavor and color of skim milk were investigated by using various techniques such as indirect competitive enzyme-linked immunosorbent assay (ic-ELISA) and Tricine-sodium dodecyl sulphate polyacrylamide gel electrophoresis (Tricine-SDS-PAGE). The results showed that the effect of AT treatment on reducing the antigenicity of the major milk allergens was significantly better than that of PT and FT treatment (P < 0.05). The antigenicity of α-lactalbumin (α-LA), β-lactoglobulin (β-LG) and casein (CN) was inhibited by 64.01%, 76.00% and 69.10% by AT treatment for 20 min at an enzyme/substrate ratio of 500 U/g, respectively. The amount of low molecular mass peptides in skim milk increased significantly after treatment with each of the three enzymes. The bitterness, astringency, aftertaste of bitterness (aftertaste-B) and aftertaste of astringency (aftertaste-A) increased with increasing enzymatic treatment time and with increasing enzyme/substrate ratio. The taste of FT-treated milk was better than that of AT- or PT-treated milk. The brightness value of milk decreased significantly, while the redness value increased significantly after enzymatic treatment (P < 0.05). The transmittance increased as well. The color of skim milk treated by AT was more similar to that of whole milk.