The aim of the present study is to assess the mefloquine-induced alteration of adult Schistosoma japonicum using confocal laser scanning microscopy (CLSM). Eight out of ten mice infected with 60-80 S. japonicum cercariae for 35 days were treated orally with mefloquine at a single dose of 400 mg/kg. Four groups of two mice were killed at 24 h and 3, 7, and 14 days post-treatment, and schistosomes were collected by perfusion from the liver and mesenteric veins, fixed in 70% alcohol, stained with acid carmine, and examined by CLSM. Worms obtained from untreated mice served as controls. Twenty-four hours post-treatment, focal tegument of adult male and female worms, which composed of fine and short villus-like materials, became thicker and longer, or disorder arrangement, while the musculatures beneath the tegument revealed in focal and irregular swelling with various degrees. In the gut of male and female schistosomes, severe dilatation accompanied by swelling, collapse, and peeling of gut mucosa was universal. In the reproductive organs, no apparent alteration in the testis structure of male worms was seen, while in female worms, slight damage to the ovary included loose arrangement of mature ovary cells accompanied by some of them degenerated and collapsed. As to vitelline glands, severe damage, such as swelling, indistinction, fusion or collapse of vitelline cells, and apparent swelling of parenchymal tissues in vitelline gland lobules, was seen. Meanwhile, abnormal ova emerged in the uterus at this time point. Three to 7 days post-treatment, the damage to the worms aggravated either in extent or in severity along with time. In some focally swollen worm body, the parenchymal tissues revealed in severe swelling. In addition, a large piece of degenerated and necrotic parenchymal tissues emerged closed to the severe destructed oral or ventral sucker. In the gut of male and female worms, the major alterations manifested by focal collapse or peeling of mucosa, and desquamation of gut epithelial cells. As to the reproductive organs, the testes of male worms revealed in reduction of size, decrease in number of germinative cells, and some of them showed degeneration and collapse, or destruction of the capsule around the testis. In female worms, some ovaries only showed degenerated and collapsed cells accompanied with many cell fragments. Meanwhile, almost all of the vitelline cells lost their definition, which revealed in indistinct cell structure, fusion of some cells, and formation of many cell fragments due to their collapse. Fourteen days post-treatment, only some male worms survived the treatment were collected. Their tegument and musculature showed prominent recovery, but severe damage to the gut and testes was still observed. Our results confirm that under the observation by CLSM, mefloquine exhibits destructive effect on adult S. japonicum, particularly the morphological structure of digestive system and reproductive system of the worms.