Temporomandibular joint disorders are prevalent causes of orofacial discomfort. Diagnosis predominantly relies on assessing the configuration and positions of temporomandibular joint components in magnetic resonance images. The complex anatomy of the temporomandibular joint, coupled with the variability in magnetic resonance image quality, often hinders an accurate diagnosis. To surmount this challenge, we developed deep learning models tailored to the automatic segmentation of temporomandibular joint components, including the temporal bone, disc, and condyle. These models underwent rigorous training and validation utilizing a dataset of 3693 magnetic resonance images from 542 patients. Upon evaluation, our ensemble model, which combines five individual models, yielded average Dice similarity coefficients of 0.867, 0.733, 0.904, and 0.952 for the temporal bone, disc, condyle, and background class during internal testing. In the external validation, the average Dice similarity coefficients values for the temporal bone, disc, condyle, and background were 0.720, 0.604, 0.800, and 0.869, respectively. When applied in a clinical setting, these artificial intelligence-augmented tools enhanced the diagnostic accuracy of physicians, especially when discerning between temporomandibular joint anterior disc displacement and osteoarthritis. In essence, automated temporomandibular joint segmentation by our deep learning approach, stands as a promising aid in refining temporomandibular joint disorders diagnosis and treatment strategies.