The objective of this work was to characterize the fat globule and milk fat globule membrane (MFGM) proteins in Maiwa (n = 6), Gannan (n = 4) and Zhongdian yak whole milks (n = 4). Fat globule size distribution and specific fat surface area of whole yak milk were determined using a laser diffraction particle size analyzer. The average specific fat surface area of Gannan yak milk (2.05 m2 ·mg−1 ) and Zhongdian yak milk (2.01 m2 ·mg−1 ) was higher (P ·mg−1 ). The total protein content of MFGM and surface protein coverage of fat globule in Maiwa yak milk (11.12 mg·g−1 fat and 5.67 mg·m−2 , respectively) and Gannan yak milk (12.24 mg·g−1 fat and 5.97 mg·m−2 , respectively) were higher (P fat and 4.81 mg·m−2 , respectively). Protein components in the MFGM of yak milk were analyzed using an Ultrascan XL laser densitometer and an LKB 2400 GelScanXL software program. No major differences (P > 0.05%) in the protein patterns on the SDS gel were observed among the MFGM of Maiwa yak, Gannan yak and Zhongdian yak, with the exception of mucin 1 and butyrophilin which were significantly lower (P < 0.05) in the MFGM of Zhongdian yak milk.