Objective To investigate the effectiveness of laparoscopic skills training based on the Smagister Living Organ Training System. Methods In September 2024, a crossover controlled trial was conducted with 12 fourth-year clinical medicine students from the Eighth Affiliated Hospital of Sun Yat-sen University. The students were randomly divided into Group A and Group B, with 6 students in each group. They underwent laparoscopic skills training using either the Smagister Living Organ Training System or the traditional dry box training method in different sequences. Comprehensive laparoscopic skills were assessed using tasks including bean picking, module threading, and knot tying/suturing (score out of 100 for each task and 300 for the total). Feedback on the training experience was collected after training. Data were analyzed using Wilcoxon signed-rank test and Mann-Whitney U test (exact method). Results Compared with the pre-training scores [120.0 (29.9) ], the first post-training scores [199.0 (41.8) ] and the second post-training scores [227.5 (48.8) ] were improved (both P<0.05). Students trained with the Smagister system showed a greater score increase in the module threading task than those trained with the traditional dry box [40.0 (15.0) vs. 20.0 (0), P=0.024]. Students trained with the traditional dry box showed a slightly greater score increase in the bean picking task than those trained with the Smagister system , though the difference was not statistically significant [31.3 (14.1) vs. 21.9 (25.0), P=0.468]. In the second test after crossover, the score increases for bean picking, module threading, and knot tying/suturing were similar between the two groups [37.5 (23.4) vs. 25.0 (21.9), 30.0 (20.0) vs. 40.0 (0), 31.5 (15.3) vs. 44.2 (18.2), all P>0.05]. All 12 students were satisfied with the laparoscopic training, and 9 were very satisfied; all students believed that the Smagister system was superior to the traditional dry box training. Conclusions The Smagister Living Organ Training System provided significant advantages for laparoscopic module threading exercises, while demonstrating comparable effectiveness to traditional dry box training method in other operational drills. This system holds valuable reference significance for enhancing the instructional outcomes of laparoscopic procedures.