[Objective] With the development of Chinese dairy industry, hay demand is increasing. As an natural forage, hay can be a carrier of livestock pathogens. The aim of this study was to investigate the bacterial community structure and the characteristics of pathogenic bacteria in hay. [Methods] We selected six different dairy farms to take hay samples. The Illumina MiSeq sequencing with 16S rRNA gene V3?V4 variable region was adopted to analyze the surface bacterial community structures of commonly used hay in dairy. [Results] A total number of 15 416 operational taxonomic units (OTUs) were obtained from hay samples under the similarity level of 97%, including 29 phyla, 87 classes, 144 orders, 219 families, and 323 genera. Microbial diversity analysis showed that hay samples had high bacterial diversity, and the diversity corresponding to each samples was specific. The results suggested that the abundance of pathogens in the natural hay was higher than that in the hay from artificial planted grasses. [Conclusion] The diversity, abundance, and characteristics of the main pathogens in hay samples were analyzed in this study, which would be a helpful reference for disease prevention and control in dairy farms.