This study examined the compatibility of 3D-printed artificial teeth and extracted teeth by combining oral cone-beam computed tomography (CBCT) and multi-jet printing technology to print the extracted teeth in vitro. The 3D-printed artificial teeth were then used to choose a master gutta-percha with an appropriate working length and taper to fill root canals. The quality of root canal-filling was evaluated via X-ray. Twenty orthodontically extracted premolars with a single root canal were collected and CBCT-scanned, and the scan data were extracted and converted to 3D models using MIMICS software, which in turn were used to 3D-print artificial teeth using multi-jet printing technology. The artificial teeth were re-scanned by CBCT to acquire 3D scan data, and the 3D deviation between the 3D-printed artificial teeth and extracted teeth was analyzed using Geomagic Studio software, in which the root canal cross-sections at 3 mm, 6 mm and 9 mm from the apex were measured and statistically analyzed. Clinically, three cases of adult anterior teeth with root canals were treated, and artificial teeth for root canal preparation were 3D-printed using multi-jet printing technology. A master gutta-percha with an appropriate working length and taper was matched and chosen to fill the root canal based on the root canal of the 3D-printed artificial tooth, and the quality of filling was evaluated by X-ray. An analysis of the 3D deviation between the 3D-printed artificial teeth prepared by combining oral CBCT and multi-jet printing technology and the original extracted teeth showed that the teeth were well-matched. There were no significant differences between the teeth regarding root canal cross-sections at 3 mm, 6 mm and 9 mm from the apex (P > 0.05). In the three clinical cases, postoperative X-ray examination showed that the root canal filling with the master gutta-percha prepared by in vitro matching based on the 3D-printed artificial teeth was good quality. The combination of CBCT and multi-jet printing technology generated accurate 3D-printed artificial teeth, which provided a master gutta-percha with a matching working length and taper for the in vivo root canal, thus providing a new approach to improve the rate of correct fill-ins in root canal fillings.