Objective: Orthognathic surgery (OGS) is a surgical intervention that corrects dentofacial deformities through the movement of maxillary and mandibular segments to achieve adequate masticatory function, joint health, and facial harmony. However, some patients present with occlusal discrepancies, condylar sag, and/or temporomandibular disorders after OGS. Various methods have been employed to solve these problems after surgery. This study aimed to evaluate the effectiveness of early screw removal in patients with occlusal discrepancies after OGS using three-dimensional cone-beam computed tomography (CBCT). Methods: In 44 patients with dentofacial deformities, patient-customized OGSs with customized plates were performed to correct facial deformities using customized guides with computer-aided surgical simulation. Of the 44 patients, eight patients complained of occlusal discrepancies and temporomandibular disorders after OGS. These eight patients underwent screw removal under local anesthesia around four weeks. The temporomandibular joint spaces at three time points (pre-surgical, post-surgical, and after screw removal) in the sagittal and coronal planes were compared using CBCT. Results: Eight patients showed an increase in joint space on CBCT images immediately after surgery (T1), but after early screw removal (T2), these spaces almost returned to their pre-surgical state, and the temporomandibular joint problem disappeared. Conclusions: The removal of screws located in the distal segment under local anesthesia between three and four weeks post-surgically may be a treatment option for patients with post-OGS occlusal discrepancies, condylar sag, and/or temporomandibular disorder.