One of the ultimate goals for orthodontic treatment is to establish an esthetic, healthy, stable and efficient occlusion. Currently, however, most of the criteria are limited to static occlusion, with little attention to dynamic occlusion. During the therapy, the orthodontists may sometimes find the maximum intercuspation(MI) is remarkably inconsistent with the centric relation(CR), or the mandibular positions are different before and after the therapy. These definitely will influence the stability of the treatment, or even the health of temporomandibular joint(TMJ) and stomatognathic system. The functional occlusion theory emphasizes that the displacement of TMJ in the glenoid fossa is the reason for the inharmony between MI and CR, and the relapse. What is more, this theory also gives the orthodontists the ways to evaluate the relationships among the MI, CR and TMJ. In this paper, we will introduce the contents and methods of the functional occlusion theory.