In the new era, the teaching of Medical Genetics requires medical students to not only master solid knowledge, but also possess practical abilities in diagnosing and treating clinical genetic diseases. This paper systematically elaborates on the design and practical exploration of teaching reform in the Medical Genetics course under the Outcome-Based Education (OBE) concept. By constructing a structured teaching system closely aligned with clinical practice, building a teaching model centered on clinical cases, carrying out diverse teaching activities, developing a “boundless classroom”, and establishing a multi-dimensional assessment system, we have achieved a deep integration of knowledge transmission and clinical reasoning training. The teaching effectiveness has shown that this model significantly enhances students’ case analysis abilities, learning motivation, and innovative capacity. However, the implementation process has also revealed deep-seated challenges in the practical teaching component, such as students facing difficulties in getting started, employing unsystematic methods, producing superficial results, and the imperfection of the evaluation mechanism. Drawing on exemplary domestic teaching cases, this paper proposes that future efforts must synergize two dimensions: “resource support” and “pedagogical design”. This involves constructing a tiered, progressive practical ability training chain, improving the faculty development support system, and exploring the use of artificial intelligence to establish process-oriented data platforms and diversified evaluation mechanisms. By putting the OBE concept into practice, we aim to promote a deep transformation of the Medical Genetics course from “knowledge transmission” to “competency development”, thereby laying a solid foundation for cultivating outstanding medical talent capable of meeting future medical demands.