Objective: To investigate the changes of environmental sanitation, health knowledge and behavior of students and diarrhea in rural schools in Henan and Sichuan Provinces from 2016 to 2018, and to provide data for improving environmental sanitation, health literacy, as well as reducing diarrhea and other infectious diseases among rural students. Methods: Based on the "Community Approach to Total Sanitation (CATS)", a total of 13 rural primary schools were selected in 2016 and 2018 respectively, including 8 in Henan and 5 in Sichuan. One class of fourth grade students was selected from each school. Totally 450 students were surveyed in 2016 and 2018, respectively. The drinking water, environmental hygiene, students personal hygiene and behavior, and the incidence of diarrhea in recent 3 months were investigated by interview, observation, inquiry and questionnaire. Results: Between 2016 and 2018, the number of schools providing safe drinking water for students increased from 6 to 8, the number of schools with proper hand washing facilities increased from 9 to 12, the number of schools with hand washing facilities equipped with soap or hand sanitizer increased from 2 to 9, and the number of schools with sanitary toilet type increased from 9 to 12. The awareness rate of students total health knowledge increased from 58.74% (793/1 350) to 64.96% (877/1 350), the formation rate of students total health behavior increased from 67.78% (1 220/1 800) to 75.28 % (1 355/1 800), the proportion of diarrhea in recent 3 months decreased from 36.89% (166/450) to 21.11% (95/450), the differences were statistically significant( χ 2=11.08, 24.86, 27.20, P <0.05). Conclusion The basic environmental sanitation facilities of rural schools in Henan and Sichuan has improved substantially, together with increased students health knowledge and hygiene behavior, and decreased incidence of students diarrhea.