The differences of temporomandibular joint (TMJ) morphologic parameters by using two-dimensional (2D) and three-dimensional (3D) measuring methods were compared. Ten asymptomatic subjects (26.75 ± 4.89 years) were randomly recruited. The 3D models of the maxilla, mandible, and teeth were reconstructed according to cone-beam computed tomography (CBCT) image data. The morphologic parameters of TMJs were measured by the 2D CBCT measuring method (group A) and the 3D reconstruction model measuring method (group B), respectively. The morphologic parameters in each group were assessed by paired samples t-test, and the statistical significance was achieved when p < 0.05. The horizontal condylar angle (HCA), sagittal ramus angle (SRA), medial joint space (MJS), lateral joint space (LJS), superior joint space (SJS), and anterior joint space (AJS) in group A were significantly smaller than those in group B (p < 0.05). The HCA on the left side was significantly smaller than that on the right side in group A (p < 0.05). However, all the morphologic parameters in group B were not significantly different between left and right sides. In conclusion, there were significant differences for the morphologic parameters of TMJ measured on 2D CBCT and 3D models. 3D measuring method should be used for the detection of TMJ morphology in clinical practice.