To investigate the effect of freeze-thaw cycles (T0: fresh meat, T1: one time freeze-thaw, T2: two times freeze-thaw) on the quality of yak meat, the yak meat samples were tested for color (L*, a*, b*), myoglobin oxidation state, metmyoglobin reducing ability (MRA), thiobarbituric acid reactive substances (TBARS), thawing loss (TL), degree of protein degradation and muscle microstructure during refrigerated storage (4℃). The T0 group showed significantly decreasing trends in a* value, b* value, oxymyoglobin (OMb) content and MRA, while significantly increasing trends were observed in metmyoglobin (MetMb) content, TBARS value and TL (P<0.05). Moreover, the degradation of myosin heavy chain (200 kDa), paramyosin (97 kDa) and actin (45 kDa) were obvious during storage. With the increase of times of freeze-thaw cycles, the a* values of T1 group and T2 group were decreased by 13.42% and 20.02% than that of T0 group after 7 d of storage, and the b* values of T1 and T2 groups were decreased by 9.94% and 16.22% (P<0.05) than that of T0 group, respectively. Meanwhile, compared with that of T0 group, the OMb contents of T1 and T2 groups were decreased by 26.30% and 53.53%, the MetMb contents of T1 and T2 groups were increased by 18.03% and 45.46% (P<0.05), respectively. The TABRS and TL of T1 and T2 groups were increased by 20.55%, 30.30% and 43.71%, 121.14% (P<0.05) than those of T0 group, respectively. The degree of protein degradation of T2 group was more serious than that of T0 group and T1 group, while the muscle microstructure damage was also increased with the increase of times of freeze-thaw cycles. In conclusion, freeze-thaw process could reduce the quality of yak meat by accelerating the deterioration of meat color, lipid oxidation and protein degradation, and damaging the muscle structure. Therefore, it is meaningful to reduce temperature fluctuation in the process of transportation and storage for protecting beef quality.