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To investigate the effect of <i>Eimeria tenella</i> (<i>E. tenella</i>) infection on the cecal microbiota, resistant and susceptible families were screened out based on the coccidiosis resistance evaluation indexes after <i>E. tenella</i> infection. Subsequently, a comparative analysis of cecal microorganisms among control, resistant, and susceptible groups as well as between different periods following the <i>E. tenella</i> challenge was conducted using metagenomic sequencing technology. The results showed that the abundance of opportunistic pathogens, such as <i>Pantoea</i>, <i>Sporomusa</i>, and <i>Pasteurella</i> in the susceptible group and <i>Helicobacter</i> and <i>Sutterella</i> in the resistant group, was significantly higher on day 27 post-inoculation (PI) (the recovery period) than on day 5 PI (the infection period). Additionally, the abundance of <i>Alistipes</i>, <i>Butyricicoccus</i>, and <i>Eubacterium</i> in the susceptible group and <i>Coprococcus</i>, <i>Roseburia</i>, <i>Butyricicoccus</i>, and <i>Lactobacillus</i> in the resistant group showed a significant upward trend during the infection period compared with that in the recovery period. On day 5 PI, the abundance of <i>Faecalibacterium</i> and <i>Lactobacillus</i> was decreased in both the resistant and susceptible groups when compared with that in the control group and was greater in the resistant group than in the susceptible group, while <i>Alistipes</i> in the susceptible group had a relatively higher abundance than that in other groups. A total of 49 biomarker taxa were identified using the linear discriminant analysis (LDA) effect size (LEfSe) method. Of these, the relative abundance of <i>Lactobacillus aviarius</i>, <i>Lactobacillus salivarius</i>, <i>Roseburia</i>, and <i>Ruminococcus gauvreauii</i> was increased in the resistant group, while <i>Bacteroides_sp__AGMB03916</i>, <i>Fusobacterium_mortiferum</i>, <i>Alistipes_sp__An31A</i>, and <i>Alistipes_sp__Marseille_P5061</i> were enriched in the susceptible group. On day 27 PI, LDA scores identified 43 biomarkers, among which the relative abundance of <i>Elusimicrobium_sp__An273</i> and <i>Desulfovibrio_sp__An276</i> was increased in the resistant group, while that of <i>Bacteroides_sp__43_108</i>, <i>Chlamydiia</i>, <i>Chlamydiales</i>, and <i>Sutterella_sp__AM11 39</i> was augmented in the susceptible group. Our results indicated that <i>E. tenella</i> infection affects the structure of the cecal microbiota during both the challenge and recovery periods. These findings will enhance the understanding of the effects of changes in the cecal microbiota on chickens after coccidia infection and provide a reference for further research on the mechanisms underlying how the intestinal microbiota influence the growth and health of chickens.