Refrigerated storage helps to ensure the quality of raw milk; however, it can also increase the risk of psychrophilic bacteria propagation. Therefore, investigation of bacterial communities of raw milk under different refrigeration durations is crucial to the sustainable development of the dairy industry. This study compared the characteristics of bacterial communities and physicochemical properties of yak milk stored at 4 ℃ for 24 h and 72 h through high-throughput sequencing and by using a milk composition analyzer. The results revealed that the two dominant bacteria in yak milk for both refrigeration durations were Lactococcus and Chryseobacterium, which together accounted for 59.5% and 67.51% of the relative abundance of bacteria in yak milk refrigerated for 24 h and 72 h, respectively. The relative abundances of Lactococcus and Chryseobacterium in yak milk were 22.74% and 3.56% higher, respectively, after 72 h of refrigeration than those in yak milk after 24 h of refrigeration. However, after 72 h of refrigeration, Streptococcus and Acinetobacter in yak milk showed a decreasing trend. The relative abundance of Pseudomonas in yak milk refrigerated for 24 h and 72 h was 1.69% and 1.78%, respectively. Casein and fat levels of yak milk refrigerated for 72 h were lower than those of yak milk refrigerated for 24 hours, and acidity increased to 14.66 ºΤ. Refrigeration for 72 h is helpful in controlling the reproduction of bacteria in yak milk to maintain milk quality. This study provides a theoretical basis for the storage of yak milk and processing of dairy products, such as cheese, to ensure quality and safety.