Objective To evaluate the value of systematic simulation training program in the training of flexible ureteroscopy. Methods The training course was divided into three parts:shifting and positioning of flexible ureteroscope, stone-grasping with basket and lithotripsy by holmium laser. Thirty trainees in the flexible ureteroscopy training class in our hospital in March 2017 were prospectively selected and divided into 2 groups:standardized systematic training group and autonomous training group, with 15 trainees in each group. The trainees in the standardized systematic training group gradually completed the training contents of the three parts in strict accordance with the contents and forms of the training courses using in vitro training dry simulator, spending 60 min in each course, while the trainees in the autonomous training group completed the training by self-study using in vitro training dry simulator for 180 min. After completing the training, the trainees in the two groups were assessed by the in vitro training dry simulator and pig animal surgery, and the examination items included the shifting and positioning of the flexible ureteroscope in the animal surgery system or the dry simulator, stone-grasping with basket, and lithotripsy by holmium laser. The operating time and global rating scale (GRS) score for the operation by tutor were compared between the two groups. Results The operating time for the shifting and positioning of the flexible ureteroscope in the animal surgery system or the dry simulator, stone-grasping with basket, and lithotripsy by holmium laser in the standardized systematic training group were significantly shorter than those in the autonomous training group (all P<0.05). The GRS scores for the above operations in the standardized systematic training group were higher than those in the autonomous training group (all P<0.05). Conclusion The systematic simulation training program divides the flexible ureteroscopy training course into three separate parts, improves the learning efficiency and enthusiasm of the trainees, helps the trainees quickly mastering the operation skills of flexible ureteroscopy, and shortens the learning curve.