The assessment of jaw movements is a common method of evaluating stomatognathic function. However, with conventional methods, detailed examination of the interrelationship between maxillofacial morphology, tooth morphology, and jaw movements is difficult. Therefore, we engineered a method of analyzing individual three-dimensional (3D) jaw movements along a time axis. This study included five adult patients with permanent dentition and no notable oral parafunctional habits who visited the orthodontic department of the Showa University Dental Hospital. We used a jaw movement analysis system to assess jaw movements during free mastication. We assessed the (1) movement trajectory of the main occluding area, (2) rate of change in the distance between the origin and the insertion of the masticatory muscles, and (3) contact patterns of the dentition. The results for (1) showed no interrelationships. For (2) , the origin and insertion of the lateral pterygoid muscle exhibited characteristic changes. The analysis of the contact pattern between the upper and lower dentition showed the contact of the molars posterior to the first premolar when masticating on the balancing side. These results indicate that jaw movements occur in a way that is appropriate for the maxillofacial morphology when food is crushed during mastication. Additionally, the occlusal contact and condylar movement during mastication may be more affected on the balancing side than on the working side. Thus, the jaw movement analysis system used in this study was useful for movement analysis during functional activity.