Objective To evaluate the efficacy of a virtual simulation system in the training of gastrointestinal endoscopy skills. Methods A self-controlled trial was conducted. From October 2018 to October 2024, 64 trainees were enrolled in a comprehensive virtual simulation training program for gastrointestinal endoscopy. The training curriculum encompassed theoretical knowledge, demonstration of operational skills, and independent practice. Comprehensive assessments of theoretical knowledge and operational skills in digestive endoscopy were performed before and after the course. Evaluation metrics included theoretical knowledge, operational skills, and trainee satisfaction, alongside the impact of the number of virtual simulation practice sessions on performance levels. Data were analyzed using paired t-tests and one-way analysis of variance. Results Following training, significant improvements were observed in the trainees' theoretical and operational skill scores for both gastroscopy and colonoscopy [Gastroscopy theory: (69.44±6.03) vs. (96.44±2.67); Operational skills: 4.00 (4.75) vs. (23.66±1.16). Colonoscopy theory: (65.98±4.16) vs. (95.69±4.77); Operational skills: 3.00 (3.75) vs. (24.47±0.84); all P<0.001]. Analysis grouped by the number of practice sessions revealed that as the sessions increased from 5 to 15, gastroscopy performance indicators (success rate of pharyngeal passage, time to intubate the duodenum, and total examination time) were progressively shortened, and the cecal intubation rate for colonoscopy continuously increased (all P<0.001). Trainee satisfaction with the training was high: regarding self-assessed learning effectiveness, 57 (89.1%) trainees gave the maximum score (5 points); regarding the enhancement of professional confidence, 55 (85.9%) trainees gave the maximum score (5 points). Conclusions The virtual simulation system proved to be highly effective in specialized digestive endoscopy skill training, significantly enhancing both theoretical knowledge and operational proficiency. A progressively increasing number of practice sessions was shown to further improve operational fluency and success rates. Trainee satisfaction was high. The virtual simulation system is confirmed to be an effective method for training specialized skills in digestive endoscopy.