Objective: To understand the toxicological indexes and indexes factors of drinking water in rural schools in Yunnan Province during 2017-2020, so as to provide scientific basis for ensuring drinking water safety, and targeted intervention in rural schools. Methods: The end water of 456，399，391，387 rural primary and secondary school drinking water supply projects in 129 counties in Yunnan Province was collected from 2017 to 2020, 11 toxicological indexes were analyzed and evaluated. Results: The overall compliance rate of drinking water toxicological indexes in rural primary and secondary schools in Yunnan Province was 99.32 %; The top three indexes exceeding the standard were nitrate nitrogen(0.31%), chloroform (0.15%) and cadmium(0.09%). The difference of compliance rate by year was statistically significant( χ 2=11.04, P <0.05); No difference in compliance rate was found between dry and wet seasons( χ 2=0.05, P >0.05); The rate of the surface water meeting the standard was higher than that of the groundwater( χ 2=9.62, P <0.05). There was no significant difference in the compliance rate between the treated and untreated projects( χ 2=1.55, P >0.05); The daily water supply scale was less than 500 m 3, and the rate of reaching the standard was lower than that of daily water supply is greater than 500 m 3( χ 2=4.27, P <0.05). Conclusion The overall percentage of the toxicological indexes in drinking water exceeding the standard in rural primary and secondary schools in Yunnan Province is low. Nitrate nitrogen, chloroform and cadmium should be considered as the prioritirized pollutants of drinking water in rural schools of Yunnan Province.