Objective: To explore the effectiveness of integrating scenario-based learning (SBL) with case-based learning (CBL) in teaching data management and analysis in medical research. Methods: Students in the preventive medicine program at Nanjing Medical University were divided into two cohorts: the 2020 cohort received CBL-only instruction, while the 2021 cohort underwent combined SBL-CBL teaching. Teaching effectiveness was evaluated through process assessment and final skill examination. Results: The SBL-CBL group achieved significantly higher final comprehensive scores than the CBL group (86.33 ± 6.37 vs. 79.50 ± 14.38). All question-type scores improved. In process assessment, the CBL group scored higher overall (17.19 ± 1.89 vs. 16.31 ± 2.04), a difference mainly attributed to peer evaluations. Conclusion: The integration of SBL and CBL has significantly enhanced students’ comprehensive data analysis skills, providing empirical evidence for teaching reform in the field of public health.