Coccidiosis poses a significant challenge to the poultry industry. However, the excessive and improper use of anticoccidial drugs and vaccines has led to resistance and food safety concerns. Consequently, traditional Chinese herbs have garnered attention as a potentially safer and more effective alternative. ChangQing compound derived from various Chinese herbal medicines is a promising anticoccidiosis agent, but its therapeutic effects have not been comprehensively evaluated. This study aimed to assess the therapeutic efficacy of ChangQing Compound against Eimeria tenella-induced coccidiosis in chickens on the basis of physiological indicators, cecum lesions, and changes in microbial diversity. The comparison with the positive control group revealed the average weight gain (AWG) and anticoccidial index (ACI) of the chicks were significantly higher, in contrast, the feed conversion ratio (FCR), cecal lesion score (CLS), and oocyst count per gram of cecal content (OPG) were significantly lower (P<0.05). Notably, AWG (138.87 g), OPG (0.57 × 106), ACI (177.92), and FCR (2.51) reflected the significant therapeutic effect of the 2.5 g/L ChangQing compound treatment (CQM). Histological sections showed that the cecal villus damage and intestinal wall swelling were minimal in the CQM, consistent with the CLS (0.73). Additionally, the 2.5 g/L ChangQing compound treatment effectively prevented the decrease of red blood cells, platelets, and hemoglobin, while promoting the release of anti-inflammatory factors interleukin-10 and interleukin-4, and inhibiting the pro-inflammatory factors interferon-γ and interleukin-17. The microbial community structure in the CQM was most similar to that of the negative control group. In summary, ChangQing compound had multiple positive effects (e.g., promoting weight gain, alleviating anemia, suppressing coccidial proliferation, reducing intestinal damage, modulating immunity, and maintaining intestinal microbiota homeostasis). The study results may be relevant to developing a novel strategy for the clinical management of coccidiosis.