Objective: To evaluate the clinical effect of root canal obturation therapy using cold flowable gutta-percha on young permanent teeth after apexification. Methods: Ninety cases of young permanent teeth with pulp necrosis or periapical periodontitis treated by apexification were randomly divided into two groups. The cases in each group were divided into single root canal and multiple root canal according to the number of the root canal, and divided into classifications Ⅰ, and Ⅱ/Ⅲ/Ⅳ according to Frank’s classification of root development after apexification. Cold flowable gutta-percha and warm gutta-percha obturation techniques were used for root canal obturation of the two groups. The operation time was recorded, and the patients’ therapy pain degree was evaluated by visual analog scale (VAS) immediately after operation. Periapical X-ray was performed after operation to evaluate the effect of the root canal filling. The total length of the root was divided into equal three parts on the X-ray film, and three-dimensional tightness of the apical, middle, and coronal region of the root canals were statistically analyzed respectively. Clinical examinations and X-ray examination were performed 6 and 12 months after the operation to evaluate the treatment success rate. Results: The operation time of cold flowable gutta-percha group was significantly lower than that of the control group, which were 51 s and 74 s (P<0.05); The percentages of pain and discomfort in the two groups were 26.67% and 40.00%, respectively. There were two cases of underfilling and no overfilling in both groups. The percentages of proper filling and tight three-dimensional obturation in the experimental and control groups were 71.11% and 60.00% respectively; and the percentages of tight three-dimensional obturation in the apical third areas were 86.67% and 66.67%, the difference was significant (P<0.05). There was no significant difference in the three-dimensional tightness between the two groups in the middle and coronal third areas. The percentages of tight three-dimensional obturation in classification Ⅰ groups were 86.67%, 83.33%, 93.33% and 76.67%, 90.00%, 96.67% in experimental and control group, respectively; The percentages of classification Ⅱ/Ⅲ/Ⅳ groups were 86.67%, 86.67%, 100.00% and 46.67%, 86.67%, 100.00%, respectively, and the difference was significant (P<0.05). There were no apical lesions that occurred in either group during the one-year review period. Conclusion: The application of cold flowable gutta-percha on young permanent teeth root canal obturation after apexification can achieve good obturation effect. The root obturation effect in the apical third area is significantly better than that of warm gutta-percha obturation techniques. Cold flowable gutta-percha can shorten the clinical treatment time and ameliorate the patients’ therapy comfort.