Objective To investigate the effect of Zanthoxylum bungeanum against Giardia duodenalis by observing inhibitory effect and structural changes on the parasite in vitro cultures by Z. bungeanum ethanol extracts. Methods Giardia strophozoites at the concentration of 7.5×10⁵-2.5×10⁶/ml in culture was treated with different concentrations of Z. bungeanum Maxim solution (0.05, 0.500, 5.00, 50.00, 250.00 mg/ml) and albendazole solution at final concentrations of 0.04, 0.40, 4.00, 40.00, and 200.00 mg/ml, respectively. A blank treatment group served as control. After anaerobic culture at 37 ℃ for 24 h using modified TYI-S-33 medium, the inhibitory effects of the two testing reagents on the growth of G. duodenalis were observed and counted. Each concentration was tested in triplicates. The half maximal inhibitory concentration (IC₅₀) values of Z. bungeanum extracts and albendazole were calculated using the SPSS 22.0 software. Then, the trophozoites of G. duodenalis were treated in vitro with the Z. bungeanum extracts at the IC₅₀ concentration for 1, 3, 7, 15 and 24 h at 37 ℃. Blank control group was set for the study. The vitality, morphological and structural changes were observed, and fatality rate of the trophozoites was calculated (repeated 3 times at each time point), and the morphological changes were observed by scanning electron microscopy.Results G. duodenalis in the blank control group showed normal growth, fullness appearance with increased number, while the Z. bungeanum Maxim at different concentrations and albendazole solution suppressed the growth of parasites. Compared with the blank control group, tthe trophozoites treated with Z. bungeanum extracts (5-250 mg/ml) and albendazole solution (0.04-200 mg/ml) showed significant morphological changes (P < 0.05). The IC ₅₀ values of Z. bungeanum extracts and albendazole were 4.57 mg/ml and 0.07 mg/ml, respectively. At the IC₅₀ concentrations, suppressive effect on the parasites was increased with longer exposure time. Exposed to the reagents for 7 h, the parasite fatality was higher than 50%, and the exposure for 15 h resulted in a fatality rate higher than 70%. The fatality reached (80.03 ± 3.62)% and (91.70 ± 4.91)% after 24 h treatment with Z. bungeanum extracts and albendazole, respectively (P < 0.05 compared with the control group). Electron microscopy found after treatment with Z. bungeanum extract for 7 h, the parasite deformed with irregular surface, but the flagella remained clearly visible; upon treatment for > 12 h, the growth of the trophozoites ceased, flagella were obviously damaged, surface cytomembrane of ventral acetabula were broken, cell content spilled, cells flattened due to losing skeleton brace; after treatment for 24, worm surface were seriously damaged, worm epithelial membrane shrank, leading to changes in worm stereo structure, and eventually leaving only the worm outer form due to depleted cytoplasm. Conclusion The Z. bungeanum extract has certain suppressive effect on the growth of G. duodenalis, and the suppressive effect on the worms was enhanced with the increasing concentration of the testing extracts.