The aim of this study was to assess the changes in individual condyles from 5 to 8 years in patients with temporomandibular joint (TMJ) osteoarthritis using 3-dimensional cone beam computed tomography (3D CBCT) reconstruction and superimposition. To assess the longitudinal TMJ changes, CBCT was performed at initial (T0) and final (T2) timepoints that were at least 5 years apart and at a middle (T1) timepoint. To improve the accuracy, we used a novel superimposition method that designated areas of coronoid process and mandibular body. The differences in the resorption and apposition amounts were calculated between each model via maximum surface distances. The greatest resorption and apposition observed were - 7.48 and 2.66 mm, respectively. Evaluation of the changes in each condyle showed that osteoarthritis leads to both resorption and apposition. Resorption was mainly observed in the superior region, while high apposition rates were observed (in decreasing order) in the posterior, lateral, and anterior regions. The medial parts showed greater apposition than the lateral parts in all regions. Our superimposition method reveals that both resorption and apposition were observed in condyles with TMJ osteoarthritis, and resorption/apposition patterns depend on the individual condyle and its sites.