With the better understanding of human genome and genetic contributions to human complex diseases, more and more clinical genetic tests have been developed for the prevention, diagnosis, and treatment of human diseases. This has raised new challenges to classroom teaching of medical genetics (MG) in medical education of undergraduates, who are relatively naive about the theory and technology of MG. A clear understanding of genotype-phenotype relationships is critical in MG learning. In the current study, we incorporated a practical approach of classroom MG teaching by using alcohol tolerance, a phenotype that is widely experienced by students and closely related to genetic polymorphism. To verify this teaching approach, which we named as student experience-based teaching (SEBT), undergraduates of two classes were recruited, with one accepting SEBT and the other accepting conventional lecture-based teaching (LBT). Final examination of the MG course indicated that while the two classes showed similar results to multiple-choice questions, the SEBT class showed significantly better performance to short-answer questions about gene polymorphism and phenotype, suggesting that SEBT might improve understanding. Thus, using student experience-based phenotypic instances and explaining the phenotype by practical genetic tests could improve understanding of genotype-phenotype relationships in classroom MG teaching.