Objective To compare the academic performance differences in the internal medicine and surgery course chains among students majoring in various clinical medicine programs, and to quantitatively evaluate their knowledge integration efficiency and the clarity of outcome-based education (OBE) achievement pathways, so as to provide evidence for targeted teaching reform. Methods Students from the entering class of 2021 at the First Clinical Medical College of Guangxi Medical University were enrolled as research subjects, including 228 students in the five-year clinical medicine program, 50 students in the "5+3" integrated clinical medicine program, and 48 students in the pediatrics program. Final written examination scores (regular examination) were collected for the courses within the surgical course chain (basic course [Regional Anatomy], bridging course [Principles of Surgery], and clinical course [Surgery]) and the internal medicine course chain (basic course [Physiology], bridging course [Diagnostics], and clinical course [Internal Medicine]). The intergroup differences in examination scores were compared through One-way ANOVA or Welch-adjusted approximate F-test, the knowledge integration efficiency was quantified by pairwise Pearson correlation coefficients between the scores of all courses within each course chain, and the clarity of OBE achievement pathways was determined by the significance of the Pearson correlations between the basic and bridging course scores, and between the bridging and clinical course scores, as well as the significance of partial correlations between the bridging and clinical course scores after controlling for the basic course scores. Results (1) Comparisons of examination scores across various programs: Significant intergroup differences were observed only in General Surgery, Surgery, and Internal Medicine examination scores (all P<0.05); specifically, students in the "5+3" integrated clinical medicine program scored lower in General Surgery but higher in Internal Medicine than those in the other two programs; students in the pediatrics program scored higher in Surgery than those in the other two programs (all P<0.05). (2) Pearson correlation and partial correlation analyses: For students in the five-year clinical medicine program, positive correlations were found only between Regional Anatomy and General Surgery (r=0.610), Regional Anatomy and Surgery (r=0.132), and Physiology and Diagnostics (r=0.515) (all P<0.05), and none of the partial correlation coefficients between bridging and clinical courses after controlling for basic course scores reached statistical significance (all P>0.05). For students in both the "5+3" integrated clinical medicine and pediatrics programs, all pairwise correlations among the courses within the internal medicine and surgical course chains were positive (all r>0, all P<0.05), and all partial correlation coefficients between bridging and clinical courses were statistically significant after controlling for basic course scores (all P<0.05). Conclusion Under the identical curricular settings, different programs' training models lead to significant heterogeneity in knowledge transfer effects. Students in the five-year clinical medicine program exhibit severe knowledge transfer discontinuity, requiring strengthened longitudinal course integration; students in the "5+3" integrated clinical medicine program show a notable weakness in key bridging course learning, necessitating explicit mapping of learning pathways; although students in the pediatrics program demonstrate high integration efficiency, caution is warranted regarding the risk of limited knowledge breadth resulting from early specialization.

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