Objective To evaluate the effect of health education on the awareness and control of clonorchiasis in primary school students in the endemic areas. Methods This study was implemented in Binyang County, Guangxi from 2017 to 2018. One primary school was selected as intervention group while another as non-intervention control group. A baseline questionnaire survey was firstly implemented in all students to understand their knowledge, practice and awareness related to clonorchiasis and the danger to eat raw fishes. Then, the comprehensive health education was carried out in the intervention group including the demonstration of an education cartoon and bulletin board on the transmission, prevention and control of clonorchiasis, distribution of educational brochure and conducting an drawing and essay competition related to the knowledge of the diseases. These educational activities did not perform in the control school. Six months later, a similar questionnaire survey were conducted to evaluate the effect of the education. Results Total 251 students in intervention group and 153 in control group participated in both baseline and evaluation surveys. In the intervention group, the awareness for the transmission route, early symptoms, complications, and carcinogenicity of clonorchiasis from 15.1% (38/251), 6.8% (17/251), 4.8% (12/251) and 4.8% (12/251) in the baseline survey significantly increased to 92.4% (232/251), 43.4% (109/251), 94.8% (238/251) and 57.8% (145/251), respectively, in the evaluation survey 6 months later, with statistical significance (P < 0.01). In contrast, in the non-intervention control group, the awareness for transmission route, early symptoms, complications, and carcinogenicity of clonorchiasis from 9.2% (14/153), 0.7% (1/153), 2.6% (4/153) and 2.6% (4/153) in the baseline survey increased to 56.9% (87/153), 33.3% (51/153), 42.5% (65/153) and 20.9% (32/153), respectively, in the evaluation survey, however, the increase was not as much as the intervention group. In intervention group, 16 students (16/251) who had history to eat raw freshwater fish during the past year in the baseline survey decreased to none to eat raw fish during the past 6 months. For those with no history to eat raw fish (235) in baseline survey, there was only one (1/235) who ate raw fish during the past 6 months. In the non-intervention control group, 35 students (35/153) who had history to eat raw freshwater fish during the past year in the baseline survey decreased to 15 to eat during the past 6 months. Out of 118 students who had not eaten raw fish, 6 had eaten raw fish during the past 6 months. The proportion of those who had history to eat raw fish but changed not to eat after baseline survey and those who had no history to eat raw fish but did after the baseline survey was significantly different between the two groups (P < 0.01). As to the awareness not to eat raw freshwater fish in future in intervention group, the rates for answering yes, no or not sure were 71.3% (179/251), 17.1% (43/251) and 11.6% (29/251), respectively, in baseline survey changed to 97.2% (244/251), 2.0% (5/251) and 0.8% (2/251) in evaluation survey (P < 0.01). In non-intervention control group, the rates of answering yes, no or not sure in the baseline survey [79.7% (122/153), 4.6% (7/153) and 15.7% (24/153)] had no significant change compared to the answers in evaluation survey [83.0% (127/153), 2.6% (4/153) and 14.4% (22/153)] (P > 0.05). Conclusion The comprehensive health education intervention in primary school students could effectively increase their knowledge and awareness to the transmission and prevention of clonorchiasis, as well as change their risk behavior to eat raw fish.