Objective To analyze the effect of orthodontics combined with oral rehabilitation on dental function and periodontal indexes in patients with congenital missing teeth. Methods A total of 85 patients with congenital missing teeth who visited the Department of Stomatology,f Chenggu County Traditional Chinese Medicine Hospital from December 2022 to December 2024 were selected and divided into the control group (n =42) and the observation group (n =43) by the random number table method. The control group was given oral rehabilitation treatment, and the observation group was given orthodontics combined with oral rehabilitation treatment. The dental function, periodontal indexes, clinical efficacy, patient satisfaction and complication rate were compared between the two groups. Results Compared with the control group, the scores of language function, dental aesthetics and masticatory function in the observation group after treatment were higher (P<0.05). Compared with the control group, the tooth mobility (TM), plaque index (PLI) and sulcus bleeding index (SBI) in the observation group after treatment were lower (P<0.05). The total effective rate of treatment in the observation group was 95.35%, which was higher than 76.19% in the control group (P<0.05). The treatment satisfaction rate in the observation group was 93.02%, which was higher than 71.43% in the control group (P<0.05). The incidence of complications in the observation group was 2.33%, which was lower than 19.05% in the control group (P <0.05). Conclusion Orthodontics combined with oral rehabilitation can effectively improve the clinical efficacy, the masticatory and language function, satisfaction and periodontal indexes of patients with congenital missing teeth, and reduce the incidence of complications.