Abstract: 【Objective】 To study the main pathogenic microorganisms of dairy cow mastitis and the distribution of microbiota in milk. 【Method】 The cows in the two farms of CJ and HZS were examined for mastitis.After visual and tactile examination of the udder and milk of the cows, 3 milk samples were randomly collected from the dairy cows diagnosed with clinical mastitis in the two farms each, and then 1 milk sample was collected from non-clinical dairy cows.Through PCR amplification and high-throughput sequencing of the 16S rRNA gene V3-V4 regions of bacteria in milk samples of mastitis dairy cows and non-clinical dairy cows, the diversity of microbial communities in clinical dairy milk samples and non-clinical dairy milk samples were analyzed and the differences were compared between the two. 【Result】 The results showed that from the 6 clinical mastitis samples, a total of 25 phyla, 47 classes, 82 orders, 174 families, and 349 genera were obtained; from 2 non-clinical dairy cow milk samples, a total of 23 phyla, 38 classes, 61 Orders, 125 families, 212 genera were obtained.In clinical mastitis samples, the dominant bacterial groups were Proteobacteria, Tenericutes, Firmicutes, Bacteroidetes, Actinobacteria; In non-clinical dairy milk samples, the dominant flora were Proteobacteria, followed by Firmicutes and Bacteroidetes.At the genus level, compared with mastitis samples, non-clinical dairy milk samples had fewer dominant bacterial groups, and only streptococcus was detected in HZS mastitis samples and Mycoplasma was detected in CJ mastitis samples. 【Conclusion】 After cows suffer from mastitis, the abundance of the microbial flora is significantly increased, and the diversity changes significantly, indicating that the milk cows suffering from mastitis will cause the milk cow's milk flora to be imbalanced, and the changes in the structure and abundance of the milk flora are closely related to the occurrence of mastitis.