This study aimed to understand long-term changes of the osteoarthritic temporomandibular joint (TMJ) condyle using computed tomography (CT) and to verify its correlation with clinical characteristics of temporomandibular disorders. Eighty-nine patients (152 joints; 76 female, 13 male) who had taken follow-up CTs (mean follow-up period: 644.58 ± 325.71 days) at least once in addition to their initial evaluation were selected. Cross-sectional demographic and clinical data and longitudinal CT images were collected. Data were analyzed by analysis of variance and logistic regression. Overall destructive change index (number of TMJ condyle sections in which destructive change was observed) decreased from 1.56 to 0.66. Improvement was seen in 93 joints (61.2%) and 27 joints (17.8%) worsened. In the pain positive group, both initial and final destructive change index were significantly higher compared to the pain negative group (p = 0.04). Occlusal stabilization splint therapy and nonsteroidal anti-inflammatory drug administration showed a significant effect on improving the prognosis of TMJ osteoarthritis (p = 0.015 and 0.011). In conclusion, TMJ osteoarthritis showed long-term improvement in the majority of cases. TMJ osteoarthritis accompanied by pain showed unfavorable prognosis with additional bone destruction. Occlusal stabilization splint and nonsteroidal anti-inflammatory drug administration were beneficial on the prognosis of TMJ osteoarthritis.