In order to elucidate the difference in the composition of milk fat globule membrane proteins (MFGMP) in bactrian camel milk and bovine milk, the high-abundance MFGMP in the two milks were determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The experimental results showed that the most abundant protein fractions in bactrian camel and bovine MFGMPs were, in decreasing order, lactophilic lipoprotein (BTN), xanthine oxidoreductase/dehydrogenase (XO/XDH), milk agglutinin (MFG-E8 or PAS6/7), and adipocyte differentiation-related protein (ADRP or perilipin-2). The results of SDS-PAGE, 2-DE and LC-MS/MS were consistent for the high-abundance MFGMP fractions from bactrian camel milk and cow milk. The bactrian camel MFGMP identified by LC-MS/MS were subjected to Gene Ontology (GO) functional annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, revealing that these proteins are mainly cell membrane, mitochondria and endoplasmic reticulum membrane components, involved in biological pathways such as translation and translation initiation, redox process, intracellular protein translocation, protein folding, and cellular redox homeostasis, and they have molecular functions such as binding activity and molecular catalysis.