SDS-PAGE was used for separating the protein components of milk fat globule membranes (MFGMs) from bovine colostrum and milk, and it was found that the compositions of milk fat globule membrane proteins in colostrum and mature milk were different. A total of 628 MFGMs were identified in bovine colostrum and 487 MFGMs in mature milk. Gene ontology (GO) annotation showed that the main role milk fat globule membranes from bovine colostrum and milk played in biological processes was biological regulation. With respect to molecular function, bovine colostrum fat globule membrane proteins had greater binding capacity than mature milk fat globule membrane proteins, and the former was found to exist much more abundantly in extracellular areas than the latter. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that both membrane proteins participated in different metabolic pathways, implicating that bovine colostrum can be further processed into high-quality products.