The immune-associated KEGG pathways in the top 20 enriched KEGG pathways included MAPK signaling pathway, cytokine–cytokine receptor interaction, metabolic pathways, endocytosis, Herpes simplex infection, and protein processing in the endoplasmic reticulum and mTOR signaling pathway, suggesting that the miRNAs play important roles in the immune response to Eimeria coccidiosis. This evidence concerns the gene MTOR and herpes simplex infectious disease.