Objective The objective of this study was to measure and analyze the joint space, condylar morphology, and thickness of the roof of the glenoid fossa (RGF) in patients with unilateral second molar scissor bite using cone beam CT (CBCT). Methods A total of 80 patients were included in this study. Forty patients with a normal posterior occlusal relationship, who attended the Department of Orthodontics at the First Hospital of Shanxi Medical University from December 2021 to August 2023, were selected as the control group. The experimental group consisted of 40 patients with unilateral second molar scissor bite during the same period. All patients underwent CBCT scanning, and the resulting images were analyzed using the NNT viewer software in multiplanar reconstruction (MPR). Axial, coronal, and sagittal adjustments were made for each patient. Results In the control group, the right and left joint spaces (PS, SS, AS), the height of the upper part of the condyle, and the depth of the glenoid fossa did not show statistically significant differences (P > 0.05). When comparing bilateral condylar morphology and joint space in the experimental group, it was found that the posterior joint space on the scissor bite side was greater than that on the normal occlusion side, while the anterior joint space on the scissor bite side was smaller than that on the normal occlusal side. Additionally, the height of the upper condyle and the depth of the glenoid fossa on the scissor bite side were greater than that on the normal occlusal side, with statistically significant differences (P < 0.05). However, there were no statistically significant differences in SS, internal and external joint diameter, as well as anterior and posterior diameters (P > 0.05). The comparison of the minimum thickness of the roof of the glenoid fossa in both the sagittal and coronal directions between the patients in the experimental group and the control group showed no statistically significant difference (P > 0.05). Furthermore, the asymmetry index of the supracondylar height in the control group was significantly smaller than that in the experimental group, displaying a statistically significant difference (P < 0.05). The differences in the asymmetry indices of the anterior and posterior diameters of the condyle, as well as the inner and outer diameters, were not statistically significant (P > 0.05). When analyzing the position of the condyle in the sagittal direction of the glenoid fossa in the patients of the control group, it was observed that the majority were in the anterior and medial positions, with only 10% and 5% being in the posterior position. However, the analysis of the condyle position in the sagittal direction of the glenoid fossa in the experimental group revealed statistically significant differences (P < 0.05), with the condyle position on the scissor bite side being more anterior. Conclusion Unilateral second molar scissor bite can result in anterior displacement of the condyle, greater height of the condyle superiorly as well as the depth of the glenoid fossa.