Objective To understand the present environmental health condition of Anhui Project county rural primary and secondary schools, provide the basis for the improvement of environmental health condition in rural schools. Methods A total of 229 primary and secondary schools in 24 counties were selected by proportional stratified randomized sampling. Results School water supply of 59.0% schools was provided by waterworks at township level or village level. 79.8% latrines in the schools were sanitary toilets. There were no any health professionals in 92.1% of the schools, and no clinics in 86.5% of the schools. There were student health records only in 25.9% of the investigated classes. Conclusion Environmental health of Anhui rural primary and secondary schools were in poor status. Improvement of environmental health of Anhui rural schools is urgent.