<p>Cystic duct malformation can increase the complexity and risk of adverse events in laparoscopic cholecystectomy (LC). The aim of this study was to detemine the benefits of training with a three-dimensional (3D) printed model of cystic duct malformation for trainees. From January 2019 to January 2024, 14 trainees were divided into two groups, the 3D training group (n = 6) and the No-3D training group (n = 6), based on whether they used a 3D-printed model for training. After the training was completed, data on LCs performed by the 12 trainees were compared to the two groups. The 3D training group completed 315 LCs within 6 months, while the No-3D training group completed 375 LCs. There were no significant differences in gender, age, or surgical experience between the two groups. In comparison to the No-3D training group, the 3D training group had a shorter operation time (35.6 ± 18.5 min vs. 39.7 ± 20.8 min, <i>P</i> = 0.007), a higher rate of recognizing cystic duct malformations (32/36, 88.9% vs. 29/48, 60.4%, <i>P</i> = 0.004), a lower rate of surgeon changes (7.3% vs. 12.5%, <i>P</i> = 0.023), and a lower incidence of total adverse events (11.1% vs. 16.5%, <i>P</i> = 0.041). Training with a 3D printed model of cystic duct malformation for junior surgeons can reduce the operation time, enhance identification of cystic duct malformations, enable trainees to complete operation independently, decrease adverse events, and improve safety.</p>