ABSTRACT Milk fat globule membrane (MFGM), primarily composed of polar lipids and numerous glycoprotein‐dominated proteins, is an emerging dairy ingredient with considerable application potential. This study systematically characterized the protein composition, structural features, nutritional properties, and digestive characteristics of three bovine milk protein materials: MFGM‐enriched whey protein (MFGMP), whey protein concentrate (WPC), and micellar casein concentrate (MCC). Label‐free quantitative proteomics identified 1025 proteins in MFGMP and 773 in WPC, with 284 differentially expressed proteins (DEPs) between them, including 247 upregulated and 37 downregulated proteins (MFGMP/WPC). Gene Ontology (GO) analysis indicated that the differentially expressed proteins (DEPs) were mainly involved in protein transport, defense response to Gram‐positive bacteria, and negative regulation of endopeptidase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed enrichment in 45 metabolic pathways, notably complement and coagulation cascades, endocytosis, and regulation of the actin cytoskeleton. Structurally, MFGMP exhibited enhanced stability, characterized by higher α‐helix and lower random coil content compared to WPC and MCC. Nutritionally, while valine was identified as the first limiting amino acid, MFGMP demonstrated a superior amino acid score and a higher essential amino acid index compared to both WPC and MCC, closely aligning with the FAO/WHO reference pattern and establishing it as a high‐quality protein source. During in vitro digestion, MFGMP showed more rapid intestinal degradation with a higher degree of hydrolysis than WPC, demonstrating superior proteolytic accessibility and digestive efficiency. These findings provide mechanistic insights into the distinctive value of MFGMP and establish a scientific basis for developing MFGM‐based functional foods.