Objective To evaluate the reliability of a new image registration technique based on CBCT images in the diagnosis and treatment of temporomandibular joint diseases. Methods The preoperative and postoperative cone beam CT (CBCT) images of 34 patients who underwent orthognathic surgery in our hospital from January 2022 to January 2023 were selected. In the open source software (3D Slicer), the voxel-based image registration technique was used to measure the position and morphological changes of the condyle, and the stability of the method was evaluated by the same type of correlation coefficient (ICC). Results The ICC of axial rotation was 0.976, the ICC of axial translation was 0.984, and the ICC of surface change was 0.947. Conclusion The new registration technique based on CBCT images has great stability in measuring condylar rotation, displacement and morphological changes, which provides a reliable evaluation for the diagnosis and treatment of temporomandibular joint diseases.