Objective: This study aims to evaluate differences in the morphological and morphometric features of hard tissue components of the temporomandibular joint (TMJ) in the cone beam computed tomography (CBCT) images of children with different skeletal models in the sagittal and vertical plane. Methods: Condyle dimensions, horizontal condylar angle, the distance of the condyle center to the midsagittal plane, condyle position, eminence height, eminence inclination, condyle, and fossa shape and symmetry were evaluated in CBCT images in 190 TMJs in 95 pediatric patients. Patients were classified as Class 1–2–3 in the sagittal direction, as hypodivergent, normodivergent, and hyperdivergent in the vertical direction. Children were divided into 10–13 and 14–17 age groups. Results: The left superior joint space in children with a different skeletal model in the sagittal plane was lower and found to be statistically significant in Class 3 children (p < 0.05). A statistically significant difference was found lower in the left articular eminence inclination and height in Class 3 children (p < 0.05). The most common oval fossa form was seen in Classes 2–3 children (p < 0.05). It was determined that the anterior joint space was lower in hyperdivergent children and the condyle was located more anteriorly. The mediolateral length of the condyle and the height of the articular eminence were positively correlated with age. Conclusions: The results revealed that the difference in skeletal models seen in sagittal and vertical planes in children may cause morphological and morphometric changes in the hard tissue components of TMJ.