To determine the effect of Qingchang Oral Liquid (QOL) on second generation merozoite of chicken E. tenella, healthy Roman pink chickens were randomly divided into model group and QOL group (drug group), and both groups of chicks were inoculated with 5×10 4 sporulated oocysts by oral gavage. Then, the drug group was given QOL at a dose of 2.4 ml/kg, and the model group was given the same volume of normal saline. After 120 hours of inoculation, both groups of experimental chickens were killed at the same time, their caecum tissues were collected, the second generation merozoite were separated, the ultramicrostructure of the second generation merozoite were observed with transmission electron microscope and the mitochondrial membrane potential and apoptosis proportion of the second generation merozoite were analyzed with flow cytometer. The current results suggested that QOL could cause swelling and vacuoles of mitochondria, swelling of endoplasmic reticulum and damage of outer membrane in the second generation merozoite of E. tenella. Compared with the model group, the drug group could increase the total apoptosis rate of the second generation merozoite (p<0.01), and reduce the depolarization rate of mitochondrial membrane potential (p<0.01). Conclusion: QOL can directly affect the outer membrane and mitochondria of the second generation merozoite of E. tenella, reduce the depolarization rate of mitochondrial membrane potential of the second generation merozoite and increase the apoptosis rate of the second generation merozoite.