Objective This study investigated the root canal morphology and determined the regularity between root and root canal in the maxillary third molar. Methods Among the 150 maxillary third molars extracted, 30 fused root teeth and 17 separated root teeth were selected for scanning from crown to apex by using micro-CT. Subsequently, a 3D visual model of teeth and their inner root canal system was reconstructed. The morphology of the root canal was observed and analyzed. Results All 17 separated root molars showed three or four canals. The number of canals in 15 of these molars was as many as that of the roots. Different types of root canals were observed in 30 fused root molars with numbers varying from 1 to 4. Conclusion Different root canal morphologies of the maxillary third molar were found. The root canals in the separated root were simple, whereas complex in those of the fused root. The number of fused root was not as many as that of the root canal.