The coccidian Eimeria necatrix infects the mid-intestine of chickens, causing hemorrhage and resulting in significant economic losses. However, there is a lack of a clear method for evaluating the tissue lesions caused by E. necatrix infection. Moreover, the impact of E. necatrix infection on gut microbiota and metabolites remains to be explored. Therefore, this study was conducted to investigate the effects of E. necatrix infection on the intestinal tissues of chickens and establish a novel histopathological scoring system for evaluating lesion severity. In addition, changes in gut microbiota and metabolites after E. necatrix infection were evaluated. Chickens aged 3 weeks were divided into 5 groups (4 experimental groups and a control group), with 6 chickens in each group. The experimental groups were orally inoculated with different concentrations of E. necatrix oocysts. Intestinal and fecal samples were collected on 7 days post-infection (DPI) and analyzed. Chickens infected with a high dose of E. necatrix exhibited diarrhea, bloody stools, and partial mortality within 6 DPI. Pathological analysis revealed a remarkable reduction in villous height, along with severe hemorrhage, necrosis, and inflammation. The histopathological scoring system revealed a strong correlation with other disease-related indicators, such as weight loss and oocyst shedding, demonstrating its stability and accuracy. Furthermore, the severity of villous lesions was closely associated with alterations in gut microbiota composition. Microbiota analysis showed a considerable reduction in the abundance of Lactobacillus in the high-dose group, whereas the abundance of potential pathogenic bacteria, including Shigella and Escherichia coli, increased, causing gut dysbiosis. Finally, metabolomic analysis indicated that E. necatrix infection disrupted energy and amino acid metabolism, particularly affecting glycolysis, the tricarboxylic acid cycle, and pyruvate metabolism. Overall, this study establishes a reliable histopathological scoring method and confirms that E. necatrix infection causes gut dysbiosis and metabolic abnormalities through tissue damage. These data provide novel insights into the diagnosis and treatment of coccidiosis in chickens.