Class III malocclusion is a combination of dental and skeletal disorders that causes discrepancies in occlusion. Malocclusion can affect the structure of the Temporomandibular joint (TMJ) resulting in many problems, one of which is affecting the internal structure of the bone. This study aimed to examine the morphological features of class III patients’ trabecular structure of the mandibular condyle in comparison with normal class I individuals using fractal analysis (FA). To study the internal structure of the mandibular condyle bone, Computed Tomography (CT) scans of 45 severe class III patients (age: 16–46) who were the candidates for orthognathic surgery were selected and matched by age and sex with 45 normal class I individuals. The trabecular bone structure of the left and right mandibular condyles in three CT planes of the study group and control group were evaluated employing the FA. The result of the present study indicated that the fractal dimensions (FD) values of class III patients were lower than those of the normal class I individuals in axial (class I: 1.31 ± 0.02, class III: 1.28 ± 0.02), sagittal (class I: 1.25 ± 0.03, class III: 1.19 ± 0.08), and coronal (class I: 1.5 ± 0.06, class III: 1.45 ± 0.07) planes (P < 0.001). There were no significant differences between the FD values of the males and females. The intra-group evaluation revealed that there was no correlation between age and FD values. No evidence of laterality was found regarding the FD values of the right and left condyles. Given the noticeable differences between the FD values, it can be implied that severe class III malocclusion may affect the trabecular pattern of the cancellous bone of the mandibular condyle compared to class I individuals. Therefore, due to the altered trabecular structure, clinicians should be cautious when planning treatments for these patients.