By the surgical orthodontic treatment for the patient who has a malocclusion, scaffold reverse occlusion, it is considered that remarkable change of maxillofacial form in the oro-facial region affects the stomatognathic functions. The purpose of this study was to analyze stomatognathic functions during border-movements and masticatory movements before and after surgical orthodontic treatment. The lateral border movements were analyzed regarding the symmetry of both sides and the change of angle of balancing condylar path. The masticatory movements were analyzed during opening and closing phases. We also analyzed cross patterns. In consequence, the lateral border movements were extended after the surgical orthodontic treatment, and the symmetries of the border-movement were improved. The angle of balancing condylar path did not show a large change in the sagittal plane by a remarkable change of the anterior guidances during lateral movements. However, the balancing condylar path in the horizontal and frontal plane had a tendency to change. The cross patterns of the masticatory movements tended to decrease after the surgical orthodontic treatment, and each of the opening phase and the closing phase tended to separated independently, i.e. each movement became stable. It was also suggested that the occlusal relationships of the upper and lower jaw including occlusal contacts had particular effect on the stomatognathic functions.