Objective: To evaluate the filling quality of single cone obturation in root canal model with irregular structure (Hus&Kim Ⅴ, Yin Ⅱ-type isthmus) which established by 3D printing technology using slices and radiographic methods, in order to provide reference for clinical practice. Methods: (1) Extracted fresh premolars with Hus&Kim Ⅴ and Yin-type Ⅱ isthmus were collected and scanned by cone-beam computed tomography (CBCT), then standard root canal models were designed and printed. Rhodamine B staining and bias fitting were used to verify the availability of the models. (2) 30 root canal models were randomly divided into 3 groups according to different filling methods (n=10). Control group: vertical compaction obturation; Experimental group 1: single cone obturation with 0.06-taper cone (30#); Experimental group 2: single cone obturation with 0.04-taper cone (35#), GuttaFlow 2 as canal sealers. Slices were taken at 2, 4, 6, and 8 mm from the root apex in the direction perpendicular to the long axis of the root and observed under a stereomicroscope to calculate the percentage of filling area (PAV), percentage of gutta-percha-filled area (PGFA), percentage of sealer filled area (PSFA). (3) On the basis of the above results, two groups (n=4) were selected to further analyze the filling quality by micro-computed tomography (Micro-CT), the filling volume of main root canal and the isthmus were obtained, and the percentage of filling volume (PFV) was calculated. Two-way ANOVA was used to evaluate the differences between the groups, and Tukey' s multiple comparison was used to compare the data between the groups and within the groups. Results: (1) Rhodamine B staining solution could overflow the apical foramen, and the main root canal system and the isthmus area were stained, showed no remnants of support material. The 3D standard deviation of the printed model data was 0.03 mm, and the average fitting distance was 0.02 mm. (2) The PFA of the two experimental groups were both significantly lower than that of the control group (F=45.04, P < 0.01). There was no statistical difference of the PFA at apical 2 and 4 mm between the two experimental groups (P>0.01), but at the middle and coronal portions of the root canal (6, 8 mm), the PFA of the experimental group 1 was higher than that of the experimental group 2 (P < 0.01). PFA in the apical 2, 4 mm of the two experimental groups were both lower than that in the middle and coronal portions 6, 8 mm of the canal (P < 0.01). There was no difference in the PGFA and PSFA between the two experimental groups at the apical 2, 4 mm (F=2.383, P>0.01). (3) The results of Micro-CT showed that the PFV of the experimental group 1 was statistically different with the control group (F=47.33, P < 0.01). The PFV of the experimental group 1 was 54.33%±4.35% in the isthmus and 78.31%±4.21% in the main root canal, which were both lower than the PFV of the control group of 76.48%±4.89% (isthmus) and 86.90%±3.29% (main root canal, P < 0.01). The PFV of the main root canal in the experimental group 1 was higher than that in the isthmus (P < 0.01), while there was no difference between the isthmus and the main root canal in the control group (P>0.01). Conclusion: In the irregular root canal structure with isthmus, using large-taper gutta-percha can improve the filling quality of the middle and upper part of the canal, but the percentage of filling volume in the isthmus is lower than that of the main canal, and more technical improvements are needed.