Orthognathic surgery including Le Fort I osteotomy involves changes in the nasal septum and maxillary sinus. This study 1) assess nasal septum changes after Le Fort I osteotomy using cone beam computed tomography (CBCT) images and 2) evaluates mucosal changes in the maxillary sinus after the surgery. This was a retrospective study of 33 patients who underwent orthognathic surgery including Le Fort I osteotomy. To assess the maxillary sinus, changes in the mucosa of the maxillary sinus were analyzed by volume and geometry. The air cavity per se and mucosal thickening of the maxillary sinus using SIMPLANT (Materialise, Belgium) software was measured. And the geometry of the distribution of the mucosa was analyzed using CBCT images. The septal angle was decreased after Le Fort I osteotomy, but not significantly (P>0.05). The volume reduction of the air cavity per se and increasing of the volume of the mucosal thickening after Le Fort I osteotomy were statistically significant (P<0.05). Mucosal thickening was observed in the posterior-inferior direction. In this study, nasal septum deviation was not statistically significant after Le Fort I osteotomy. The changes of the maxillary sinus after the Le Fort I osteotomy is inevitable. But the studies that take into consideration of the importance of the evaluation of nasal septum and maxillary sinus were insufficient. Using CBCT images we evaluated pre and post-operative changes of the nasal septum and maxillary sinus. Decrease of the air cavity per se, decrease of the total volume of the maxillary sinus, and increase of mucosal thickening were prominent. Furthermore, the mucosal thickening that occurs after surgery appears to be mainly in the posterior lower part of the maxillary sinus.