Objective: To understand rural school toilet sanitation conditions in Chongqing during the year of 2015 to 2017. Methods: One primary school and one secondary school from each village were selected from five villages of each district. A total of 265 rural schools from 10 districts of Chongqing including 144 primary and 121 secondary schools were selected. Data was collected through access to information, field observations and onsite interview. Results: The sanitation coverage rate was 78.45%, 92.99%, 100% from 2015 to 2017, respectively. The coverage rate in teaching building was the lowest(43.02%, 51.65% and 57.95% from 2015 to 2017, respectively). Male toilets in secondary schools showed high quality(92.38%, 92.86%, 100.00% for the year of 2015, 2016 and 2017, respectively). However, the quality of female toilets in middle schools was poor(33.33%, 53.06% and 68.00% for the year of 2015, 2016 and 2017, respectively). Daily sanitation management enhanced by year(29.07%, 40.66% and 69.32% during 2015 to 2017). Soap provision in school toilets decreased with year (53.49%, 40.66% and 1.14% for the year of 2015 to 2017, respectively). Conclusion In the past three years, sanitation condition of rural school toilets in Chongqing has significantly improved. However, toilets in the teaching buildings and dormitories are relatively insufficient. More femalefriendly toilet seats and daily sanitation management require further investment.