Different breeds of cows affect the form of fat exist in dairy products and the final functionality, which depended mainly on the composition of the milk fat globules(MFG). However, the relationship between the composition and breeds has not been illuminated. In our study, differences in the lipid content and fatty acid composition of native bovine, buffalo and yak MFG were investigated by confocal Raman spectroscopy. The research offers the possibility of acquisition and analysis of the Raman signal without disruption of the structure of fat globule. The results showed that yak MFG had a higher ratio of band intensities at 2 885/2 850 cm-1, indicating yak MFG tend to have a triglyceride core in a fluid state with a milk fat globule membrane in a crystalline state. The buffalo and yak MFG had a higher level of unsaturation compared to bovine MFG, shown by a higher ratio of band intensities at 1 655/1 744 cm-1. The results indicate that small MFG of buffalo is more unsaturated than yak, while the large MFG of buffalo is less unsaturated than the yak. Thus, selective use of cream with yak MFG would allow a harder and more costly churning process but lead to a softer butter. Buffalo milk which contains larger MFG is more suitable for cream and MFG membrane separation.