Objective To study the application value of cone beam CT in orthodontic treatment. Methods From March 2023 to January 2024, 69 orthodontic patients who were treated in the 80th Group Army Hospital were selected as the research objects. According to the random number table method, they were divided into control group (n =34) and study group (n =35). The control group underwent X-ray examination in orthodontic treatment, and the study group underwent cone beam CT examination in orthodontic treatment. The maxillofacial improvement, dental function and oral related index scores were compared between the two groups. Results After treatment, the indexes of SNB, SNA and ANB in the study group were better than those in the control group (P <0.05). After treatment, the scores of swallowing, masticatory and language function in the study group were higher than those in the control group , and the difference was statistically significant (P <0.05). After treatment, the scores of teeth neatness, occlusal contact and anterior teeth coverage in the study group were higher than those in the control group, and the difference was statistically significant (P <0.05). Conclusion Cone beam CT in orthodontic treatment can effectively improve the tooth function of patients, and clarify the head shadow index of upper and lower jaws, which is conducive to improving the treatment of oral related indicators.