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Abstract Background Basic surgical skills (BSS) is a key bridging course for medical students to acquire basic surgical maneuvers and practice animal surgery before clinical rotation, but the complexity of operational procedures and high demands on asepsis may lead to poor performance and frequent error during practice. The current study intended to improve BSS teaching outcomes by implementing smartphone app-based competency and performance checklists for medical academy undergraduates. Methods WeChat-based checklists containing competency and performance modules were designed, distributed and collected via smartphone. One hundred seventy-six third-grade undergraduate cadets majoring in clinical medicine or anesthesiology were prospectively enrolled, with 92 set as study group and 84 as control group. Checklists were distributed for self-evaluation before and after each class throughout the semester of autumn 2021-2022. Student age, previous Grade Point Average (GPA), average grades of BSS (including grade-A rate and pass rate), operative time, error rate, and perioperative complications of intestinal anastomosis performed on Beagle dogs between the groups were compared to evaluate the efficacy of the checklists. Results The students aged 20.2 ± 0.63 in Group A and 20.3 ± 0.92 in Group B (P = 0.15), with a previous GPA of 2.9 ± 0.61 vs. 2.87 ± 0.58 (P = 0.61). The average operative time on their final lesson of intestinal anastomosis was 192.3 ± 27.18 min vs. 213.8 ± 29.48 min (P < 0.001). All students passed in BSS course, with a final grade of 89.45 ± 4.360 in Group A and 86.64 ± 4.026 in Group B (P < 0.001), in which grade-A rate was 46.7% vs. 26.2% (P = 0.005). For perioperative comorbidities, 4/23 (17.4%) animals in Group A and 5/21 (23.8%) in Group B recorded wound dehiscence or other incision-related complications; no animals died in Group A, and 2 died in Group B due to hemorrhagic shock or sepsis. Conclusions The implementation of WeChat-based checklist is a reflection of improved quality of teaching in BSS course that may promote the students’ competency and performance.