To explore the application effect of FR-Ⅲ functional orthodontic appliance in children with anterior crossbite. Methods Sixty children with anterior crossbite admitted to our hospital from January 2020 to January 2023 were selected as the research objects. They were divided into control group and experimental group by random number table method, with 30 children in each group. The control group was treated with straight wire fixed appliance, and the experimental group was treated with FR-Ⅲ functional orthodontic appliance. The clinical efficacy, cephalometric results and Children Behavior Checklist Scale (CBCL) scores were compared between the two groups. Results The total effective rate of treatment in the experimental group was 96.67%, which was higher than 66.67% in the control group, and the difference was statistically significant (P <0.05). After treatment, the SNA angle and SNB angle of the experimental group were larger than those of the control group, while the ANB angle and U1-SN angle were smaller than those of the control group, and the differences were statistically significant (P <0.05). After treatment, the CBCL score of the experimental group was lower than that of the control group, and the difference was statistically significant (P <0.05). Conclusion Compared with the conventional straight wire fixed appliance, FR-Ⅲ functional orthodontic appliance is more effective in the treatment of anterior crossbite in children, which can effectively improve the facial morphology and psychological behavior of children, and is worthy of clinical application.