Purpose This study sought to assess the relationships between a morphological characteristic of the superior semicircular canal (SSC) and both the roof thickness of the glenoid fossa (GF) and bone changes of the temporomandibular joint (TMJ) on three-dimensional images. Methods Cone-beam computed tomography (CBCT) images of 200 individuals (105 females and 95 males; 400 temporal bone regions) were examined by two different observers. The correlations between the bone thickness overlying the SSC and the thickness of the roof of the GF with TMJ's bone pathologies were analyzed. Results The superior semicircular canal dehiscence (SSCD) was significantly associated with dehiscence of the roof of the GF. The relationship between the dehiscence of the SSC and the roof thickness of the GF was found to be strongly correlated (p < 0.05). There were no statistically significant differences between the bone changes of TMJ and the presence or absence of the SSCD. Conclusions A correlation between the bone thickness overlying the SSC and the roof thickness of the GF was found. However, there was no relationship between the bone thickness overlying the SSC and bone changes of TMJ.