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Bacterial enteritis is the most important disease in lamb for breeding greatly affects the growth of animals. Changes in the community of intestinal flora can cause the disorder of the colonic environment induced diarrhea. This study aimed to investigate the relationship between the incidence of bacterial enteritis and the number of intestinal microbiome, then the prevalence of drug-resistant genes was detected. Fecal samples were collected at five fattening sheep farms with different incidence of bacterial enteritis, pathogenic bacteria were isolated and identified, drug sensitivity tests were performed. Then, changes in number and structure of intestinal flora were compared by 16S rDNA V3-V4 region high-throughput sequencing, and the ARGs were detected using high-throughput real-time PCR. Our results revealed that the microbial communities were positively correlated with the incidence of bacterial enteritis in different farms. Bacterial communities were higher in YJ (with highest incidence of diarrhea) than any other farms. However, the ARGs seemed not to be more affected by the incidence of bacterial enteritis, but one of the significant findings to emerge from this study is that MCR-1 and NDM are detected in manure. This study has provided an insight of the changes occurring in intestinal flora and AGRs in fattening sheep farms with diverse incidence of bacterial enteritis.