Objectives: During Le Fort I osteotomy, the separation of the pterygomaxillary junction (PMJ) is a difficult procedure for most surgeons because it is invisible. In this process, damage to the posterior structures constituting the sinus or those adjacent to it, including the maxillary sinus posterior wall and pterygoid plate, may occur. We would like to investigate the effects of this on the inside of the maxillary sinus after surgery and whether there are complications. Materials and Methods: One-hundred patients who underwent Le Fort I osteotomy from 2013 to 2020 using cone-beam computed tomography images were classified into two groups (clean-cut type and fractured type) according to the PMJ cutting pattern. In addition, the mucosal thickness in the maxillary sinus was divided into preoperative, postoperative three months, one year, and the change over the course of surgery was evaluated retrospectively. Results: Of the total 100 cases, the clean-cut type numbered 28 cases and the fractured type totaled 72 cases. Among the fracture types, part of the sinus wall and the pterygoid plate were broken in 69 cases, and the maxillary sinus posterior wall was detached in three cases. There was no statistically significant difference in sinus mucosal thickening between the clean-cut type and fractured type of the PMJ, three months and one year after surgery between the two groups. However, there was a significant difference in sinus mucosal thickness at postoperative one year in the case where a partial detachment of the maxillary sinus posterior wall occurred compared to not. Conclusion Even if there is some damage to the structures behind the PMJ, it may not be reasonable to spend some time on the PMJ separation process considering the overall postoperative complications, if there is no significant difference inside the sinus, or increased probability of postoperative complications.