Objective <p>To investigate the condylar joint space, position and morphology in skeletal Class II malocclusion patients with idiopathic condylar resorption (ICR), in order to provide reference for the clinical treatment and efficacy evaluation of ICR.</p> Materials and methods <p>Skeletal Class II malocclusion patients with ICR and skeletal Class II malocclusion patients with normal temporomandibular joint (TMJ) structure were included in this study. The anterior joint space (AJS), superior joint space (SJS) and posterior joint space (PJS) were measured by computed tomography (CT) and magnetic resonance imaging (MRI). The surface area and volume of condyle were measured through three-dimensional reconstruction using CT scans.</p> Results <p>A total of 55 patients were included in both groups. All ICR patients exhibited bilateral anterior disc displacement without reduction (ADDWOR), with MRI revealing morphological changes in 90.91% of ICR patients. SJS in ICR group significantly decreased by 15.85% on CT and 14.23% on MRI (<i>P</i>&lt;0.05). The typical SJS-PJS difference in healthy TMJs disappeared in ICR patients, and joint space proportions became irregular, indicating condylar instability. Mild resorption was found in 78.18% of ICR patients, mainly affecting the anterior slope and condylar apex, while 21.82% showed more severe resorption. Condylar ratio in ICR patients showed greater variability, reflecting increased instability. Additionally, condylar volume and surface area were significantly reduced by 29.9% and 21.3%, respectively (<i>P</i>&lt;0.05).</p> Conclusion <p>ICR patients show varying levels of condylar resorption and less consistent joint space proportions. These findings may reveal the influence of resorptive morphological changes on the stability of condylar position within the glenoid fossa.</p> Trial registration <p>This study was registered at the Chinese Clinical Trial Registry (ChiCTR2100051867) on October 8, 2021.</p>