Microbial aerosol particles carried in chicken coops are a major cause of respiratory diseases in both poultry and workers. This study aimed to investigate the microbial community structure in microbial aerosol particles under three different feeding methods and analyze the composition of the bacterial community in the air of chicken coops using high-throughput sequencing. The results revealed that the dominant phyla in all samples were Firmicutes, Proteus, Actinomyces, and Bacteroides. Among these, Firmicutes had a higher proportion in the coop air. However, at the genus level, there were significant differences in microbial species among the three rearing practices. Additionally, potential pathogenic bacteria were found in the coop air, including Staphylococcus, Acinetobacter, Streptococcus, Flavobacterium, Clostridium, Rhodococcus, and Campylobacter. In conclusion, the air in chicken coops contains various types of small and medium-sized microorganisms, including some pathogenic bacteria that can infect livestock, poultry, and breeding staff. It is recommended to utilize thick bedding feeding and cage feeding methods while also strengthening cleaning and disinfection protocols in the chicken coops.