Objective To understand the status of oral health and its influencing factors among 12-year-old children in Chongqing, so as to provide evidence for setting up the intervention policy of oral health for children. Methods The data obtained from "the assessment on the comprehensive intervention effect for oral health among children in Chongqing" in 2015 were used in the present study; multi-level logistic regression model was used to analyze the status of oral health and its influencing factors among children in Chongqing. Results The prevalence of dental caries among 12-year-old children was 45.5% (922/2 025) in Chongqing, and the status of oral health was clustered at school level (Ω_u=0.412, P=0.091, α=0.1). Multi-level logistic regression analysis indicated that the gender, sugar or chocolate intake once a week and above, and "whether children recognizing that oral health is very important for their life" were the individual variables affecting the dental caries incidence in 12-year-old children, and the difference between urban and rural schools was its background variable (P<0.05, α=0.05). Conclusion The gender, cognition to oral health, behavioral habit and the difference between urban and rural schools where children study are important factors influencing the oral health of 12-year-old children in Chongqing, and pertinent measures should be taken to improve the oral health among children.