Males with TMJOA showed a posteriorly positioned and backward-rotated mandible, especially in skeletal Class II adults. Compared with women, the craniofacial morphology of men is less affected by TMJOA. The association between TMJOA and craniofacial morphology also varied across different age groups and skeletal patterns. Prospective studies are required to clarify the cause-effect relationship between TMJOA and craniofacial morphology in males.