60 healthy Roman powder chickens were randomly divided into normal group and model group, 30 in each group with 30 chickens in each group. The model group was fed with 1×104 sporulated oocysts to artificially replicate the chicken coccidiosis model. The normal group was treated with normal saline. Five days after infection, the test chickens were sacrificed, the contents of the chicken cecum were collected aseptically, and the 16S rDNA gene V3-V4 variable region of the intestinal flora of the cecal contents of broilers was detected by Illumina PE250 high-throughput sequencer. Comprehensive analysis and evaluation of the number of operable taxonomic units(OTUs) of the intestinal flora, α and β diversity, as well as differences in phylum and genus, to study the effect of Eimeria tenella infection on the structure and diversity of chicken cecal flora. The results showed as follows: after infection with Eimeria tenella, the number of OTUs and the Chao1 index in the model group decreased extremely significantly, and Shannon index in the model group decreased significantly, the Simpson index increased significantly. The composition of the bacteria group: at the phylum level, the abundance of Proteobacteria in the model group was increased extremely significantly, while that of Firmicutes was reduced extremely significantly. At the genus level, the predominant bacteria in the normal group were Bacteroides, Ruminococcaceae-UCG014, and Parabacteroides; in the model group, the relative abundance of Ruminococcaceae_ uncultured, Tyzzerella and Escherichia-Shigella increased extremely significantly. Eimeria tenella disrupted the integrity of the cecal microbiota and promotes the establishment and growth of potentially pathogenic bacteria, especially the growth of Escherichia-Shigella.