Objective To explore the intervention effects of targeted health education on the knowledge of echinococcosis prevention and treatment and the practice rate of healthy behavior among students, and provide reference for implementation of health education of echinococcosis on classified base. Methods All students in the central primary schools in Bamei and Longdeng Townships in Daofu County, were assigned as the intervention group, and all students in the central primary school Qimei and Xianshui Townships were assigned as the control group. From 2016 to 2020, students in the control group were provided with conventional echinococcosis health education, and students in the intervention group were provided with additional special interventions. In each year, 150 students randomly selected from each grade of grades 3-6 in each school were surveyed. A questionnaire was used to assess the awareness rate of knowledge of echinococcosis control and the formation rate of health behavior among the students. Results In 2016, before the intervention, the awareness rates of knowledge of echinococcosis control in the intervention and control groups were 77.0% and 74.3%, respectively, and the formation rates of health behavior were 68.5% and 70.6%, respectively, with no significant difference between the two groups (P > 0.05). After the intervention, the awareness rate and behavior formation rate of students in both groups increased from 82.8% and 71.9% in 2017 to 93.1% and 85.5% in 2020, respectively (P < 0.05), and the intervention effect was better in the intervention group compared with the control group. The difference in the knowledge awareness rate between the two groups began to be significant in the first year after the intervention (82.8% and 77.4% in 2017) (P < 0.05), while the difference in the behavior formation rate began to be significant in the second year (78.5% and 75.1% in 2018) (P < 0.05), with a significant lagging response in behavior formation. In the control group, the awareness rate and behavior formation rate did not show significant difference between different years (P > 0.05), while in the intervention group, the awareness rate and behavior formation rate showed significant differences during 2016—2019 and 2017—2019, respectively (P < 0.05). Meanwhile, the awareness rate and behavior formation rate of students in the intervention group did not show significant difference between 2019 and 2020 (P > 0.05), indicating the intervention had gained steady achievements. The stratified analysis on the results demonstrated that after 4 year-consecutive health education, the difference in awareness rate between the intervention group and the control group was statistically significant in both boys and girls in 2020 (P < 0.05). The difference in awareness rate between the intervention group and the control group was statistically significant in all grades from 3 to 6 (P < 0.05). The difference in awareness rate between the intervention and the control groups was statistically significant in both Han Chinese and Tibetans (P < 0.05). There was no significant difference between the two groups in other ethnicities (P > 0.05). In addition, there was a significant difference in behavior formation rate between the intervention group and the control group in girls (P < 0.05). There was a significant difference in behavior formation rate between the intervention group and the control group in grades 4-6 (P < 0.05). Statistically significant differences in the behavior formation rate between the intervention and control groups were found in Tibetan and Han Chinese (P < 0.05). There was no significant difference between the two groups in male students, at grade 3, or in other ethnic groups (P > 0.05). Conclusion The health education pertinent to students can help improving their awareness of echinococcosis knowledge and forming health behavioral habits.