Objectives: This study used cone-beam computed tomography (CBCT) images to categorize the relationships between the mandibular canal and the roots and investigated the prevalence of nerve damage. Materials and Methods: Through CBCT images, contact and three-dimensional positional relationships between the roots of the mandibular third molar and the mandibular canal were investigated. With this data, prevalence of nerve damage according to the presence of contact and three-dimensional positional relationships was studied. Other factors that affected the prevalence of nerve damage were also investigated. Results: When the mandibular third molar and the mandibular canal were shown to have direct contact in CBCT images, the prevalence of nerve damage was higher than in other cases. Also, in cases where the mandibular canal was horizontally lingual to the mandibular third molar and the mandibular canal was vertically at the cervical level of the mandibular third molar, the prevalence of nerve damage was higher than in opposite cases. The percentage of mandibular canal contact with the roots of the mandibular third molar was higher when the mandibular canal was horizontally lingual to the mandibular third molar. Finally, the prevalence of nerve damage was higher when the diameter of the mandibular canal lumen suddenly decreased at the contact area between the mandibular canal and the roots, as shown in CBCT images. Conclusion: The three-dimensional relationship of the mandibular third molar and the mandibular canal can help predict nerve damage and can guide patient expectations of the possibility and extent of nerve damage.