Objective To apply ADA caries risk assessment for caries classification management in children aged 3-6 years old, and to evaluate its clinical application effect. Methods A total of 120 children aged 3-6 years old who were treated in the Department of Pediatric Stomatology, Stomatological Hospital of Tianjin Medical University from July to October 2020 were randomly divided into experimental group and control group, with 60 children in each group. The experimental group was evaluated according to the ADA caries risk assessment system proposed by the American Dental Association (ADA), and individualized and multi-dimensional early biological prevention and clinical treatment were carried out according to the risk level. The control group was given basic oral clinical treatment. The incidence of dental caries in the two groups was observed after 1 year of intervention. Results The caries rate of the experimental group was 88.33%, which was higher than 86.67% of the control group, and the difference was not statistically significant (P >0.05). After 1 year of caries classification management, the incidence of caries in the experimental group was 3.33%, and the new caries was 0.05, which was lower than 18.33% and 0.22 in the control group, the difference was statistically significant (P <0.05). Conclusion ADA caries risk assessment can effectively reduce the incidence of caries in children aged 3-6 years old.