Background: As a multifactorial disorder, temporomandibular joint (TMD) is difficult to diagnose, and multiple factors affect the joint and cause the temporomandibular disorder. Standardization of clinical diagnosis of TMD should be used to reach a definite clinical diagnosis; the condylar bone may degenerate in accordance with these disorders. Aims: Evaluate the correlation between the clinical diagnosis and degenerative condylar change (flattening, sclerosis, erosion, and osteophyte). Materials and Methods: A prospective study with a study group of 97 TMD patients (total of 194 joints) aged 20 to 50. Patients were sent to cone beam computed tomography (CBCT) to assess the degenerative condylar change. Results: No association was found between the clinical diagnosis of TMD with osteophyte and sclerosis. While there was a significant association was found between flattening and erosion and clinical diagnosis. Conclusions: Disc displacement with reduction was the most frequent TMDs. Erosion and flattening were the most frequent bone change found among the different subgroups of clinical diagnosis. Erosion was frequently seen in degenerative joint disease (DJD) with a significant association. While flattening was mostly found in disc displacement without reduction without limited mouth opening (DDwoR without limited) with a significant association.