Anatomy forms the foundation for the training and execution of routine surgical procedures. However, a gap persists in effectively bridging anatomical knowledge with the confident performance of procedures. Virtual simulation (VS) techniques, based on experiential and situated learning theory, hold promise in addressing this challenge. Apicoectomy, a procedure involving root apex resection to preserve a tooth, requires a blend of regional and dental anatomy knowledge, making it an ideal model for assessing the effectiveness of VS. This prospective cohort study evaluated primarily the enhancement of incorporating VS training in the preclinical skill training of apicoectomy for undergraduate dental students, compared to relying solely on traditional methods. VS training includes the simulated dissection process, patient examination, and apicoectomy based on graphically synthesized virtual models. Secondly, the study investigated the influence of exposure to VS training on students' confidence and satisfaction. The training was divided into three progressive levels aligned with students' cognitive processes, employing Miller's competence learning framework. Participants were categorized into the control group (CG) (n = 214) and VS training group (VSTG) (n = 220) based on their classes. The results demonstrated that VSTG showed significantly greater training enhancement (VSTG: 7.14 ± 1.74; CG: 6.57 ± 2.02, p = 0.002) and higher confidence levels (VSTG: 2.94 ± 0.13; CG: 2.69 ± 0.13, p < 0.001), along with greater satisfaction with the training compared to the CG (VSTG: 3.70 ± 0.18; CG: 3.20 ± 0.17, p < 0.001). In conclusion, VS proves to be a valuable adjunct for enhancing procedural skill training in surgical procedures.