Objective The aim of this study was to investigate the use of 3D microstructural bone analysis in patients with degenerative joint disorder (DJD) to enhance the diagnostic capacity of cone beam computed tomography (CBCT) in the evaluation of bone tissue. Methods 147 TMJ CBCT images of 88 participants were assessed with regard to DJD in the mandibular condyle. We divided each condyle into 3 groups (0, 1, 2) according to diagnosis of DJD: 0 indicates normal condyles (control individuals), 1 indicates mild erosive osteoarthritic change (EOC) and 2 indicates severe EOC. 3D fractal dimension (FD) was calculated on CBCT images of mandibular condyle and were compared with the radiographic diagnosis of patients. Results ANOVA test showed that there was statistically significant difference in FD values among each groups. The average FD value of group 0 was 1.971, group 1 was 1.918 and group 2 was 1.863. Lower FD values and more severe degenerative changes were seen in patient group 2. To evaluate the reliability of fractal analysis (FA) method, receiver operating characteristic (ROC) curve analysis was performed. Area under the curve (AUC) was 0.717 (p < 0.001). Conclusion This study provides a preliminary conclusion that fractal analysis may be a helpful tool to enhance the diagnostic capacity of CBCT in the evaluation of DJD.