In this study, the bioinformatics software DNAStar and Geneious and multiple reaction monitoring mass spectrometry (MRM-MS) were used to predict the linear epitope parameters, secondary structure content and epitope regions of bovine whey proteins. Meanwhile, relative quantification of linear allergenic epitopes was carried out. The results indicated that α-lactalbumin (α-LA) and β-lactoglobulin (β-LG) had 7 and 10 linear epitope regions, respectively. The secondary structure of α-LA and β-LG mainly consisted of α-helix, followed by β-turn, β-sheet and random curling, indicating that the structure of α-LA and β-LG made them more likely to become epitopes. Alkaline, protamex and flavourzyme treatment effectively reduced the linear allergenic epitopes of α-LA and β-LG by 50.0%-80.0%, with this effect being more pronounced for β-LG. The relative quantitation results showed that the content of 95.0% of linear epitope peptides was significantly reduced.