The treatment of dentofacial deformities generally includes orthognathic surgery in which mandibular condyle changes following surgery are a common cause of relapse. This study investigated the changes in the mandibular condyle and related muscles to identify the factors that affected the changes in the mandibular condyle after orthognathic surgery in skeletal class II patients. This research studied 60 joints in 30 patients with skeletal class II dentofacial deformities who received surgical orthodontic treatment, including bilateral sagittal split ramus osteotomy, and underwent computed tomography before and after orthodontic treatment. The mandibular condyle, masseter, and medial pterygoid muscles were reconstructed and measured in 3D. Condylar positional and morphology changes, masseter and medial pterygoid muscle volume, temporomandibular joint (TMJ) pain, and distal segment movement were analyzed. The study observed that both the masseter and medial pterygoid muscle volumes decreased with statistical significance. The changes in the horizontal direction were positively correlated with the amount of movement. The findings indicated that mandibular condyle changes were significantly affected by the movement of the distal segment, the medial pterygoid muscle volume, and the direction of the distal segment, which influenced the treatment’s long-term stability after orthognathic surgery.