To investigate three-dimensionally using cone beam computed tomography (CBCT) morphological and spatial characteristics of the temporomandibular joints (TMJs) in different anteroposterior skeletal malocclusions.Pretreatment CBCT scans of 60 young adult patients (18–25 years) were obtained. Among those patients, 20 were characterized as Skeletal Class I, 20 as Skeletal Class II, and 20 as Skeletal Class III malocclusion. Bilateral TMJs were evaluated on the CBCT images and the following three-dimensional measurements were assessed: (1) mandibular fossa position, inclination, and parameters; (2) mandibular condyle position, inclination, and parameters; and (3) circumferential TMJ space measurements.Class II patients showed the lowest condylar width (6.47 ± 1.14 mm), the highest condylar height (11.14 ± 1.99 mm), and the highest anterior joint space (2.73 ± 1.14 mm). Class III patients exhibited the lowest anterior (2 ± 0.57 mm), superior (2.92 ± 0.63 mm), and medial joint spaces (2.18 ± 0.72 mm), and the highest mandibular fossa width (19.12 ± 2.48 mm), as well as the highest anteroposterior condylar dimension (7.43 ± 1.50 mm). The three skeletal malocclusions differed significantly in the vertical condylar position (Class III had the most superior and Class II had the most inferior position).There are significant differences in specific TMJ parameters between different skeletal malocclusions that might play a role in development of temporomandibular disorders with or without orthodontic treatment.