To investigate the effect of bracketless invisible correction and traditional fixed correction in orthodontic treatment of children with malocclusion. Methods A total of 90 children with malocclusion who underwent orthodontic treatment in our hospital from April 2018 to April 2023 were selected as the research objects. According to the different treatment schemes, they were divided into control group and study group, with 45 children in each group. The control group was treated with traditional fixed orthodontics, and the study group was treated with bracketless invisible orthodontics. The clinical efficacy, periodontal health indicators, treatment satisfaction and complications were compared between the two groups. Results The total effective rate of treatment in the study group was 95.56%, which was higher than 77.78% in the control group, and the difference was statistically significant (P <0.05). After treatment, the gingival crevicular depth, gingival index, gingival sulcus bleeding index and plaque index of the study group were better than those of the control group, and the differences were statistically significant (P <0.05). The satisfaction scores and full scores of comfort, appearance, convenience and chewing function in the study group were higher than those in the control group, and the differences were statistically significant (P <0.05). The incidence of complications in the study group was 4.44%, which was lower than 20.00% in the control group, the difference was statistically significant (P <0.05). Conclusion The effect of bracketless invisible orthodontic treatment in orthodontic treatment of children with malocclusion is better than that of traditional fixed orthodontic treatment, which is more conducive to improving the periodontal health status of patients, with fewer complications and higher treatment satisfaction.