Background The purpose of this study was to analyze root migration and its influencing factors at 6 months after coronectomy in both two- and three-dimensions using periapical view and cone-beam computed tomography (CBCT). Methods Thrity-three cases of root remnant after coronectomy were included and analyzed. We measured the amount of migration in CBCT. The following factors that could possibly affect root migration were also analyzed: age, gender, number of mandibular third molar (M3) roots, shape of M3s, Pell and Gregory classification, mesiodistal (MD) angulation, buccolingual (BL) angulation, contact point with the second molar, root curvature, and complete removal of the coronal portion. Results Migration of greater than 2 mm was found in 64% of the roots in the 2D analysis, and the average root migration was 4.11 mm in the 3D analysis. The factors affecting migration were the root morphology, complete removal of the coronal portion, impaction depth, and MD angulation in the 2D analysis, and MD and BL angulation in the 3D analysis. Conclusion In conclusion, complete removal of the coronal portion and ensuring sufficient space for root migration might be important factors after coronectomy of the M3. Clinical relevance Root remnant after coronectomy of M3 may migrate in young patients who has sufficient empty coronal space and this may reduce the nerve damage by the separation of IAN and M3.