As a core course for pharmacy majors, medicinal chemistry is of great importance. Traditional rote memorization-based teaching methods focus on basic knowledge but neglect the cultivation of students’ innovative thinking and problem-solving abilities, making it difficult to meet the demand for innovative pharmacy talents under the interdisciplinary development of “New Engineering, New Medicine, New Agriculture, and New Liberal Arts”. Accordingly, there is an urgent need to redesign the course to emphasize “higher-order, innovation and challenge” (“Two Characteristics and One Degree”), fostering students’ independent thinking and creativity. However, identifying discussion topics and conducting effective classroom discussions that reflect the “Two Characteristics and One Degree” teaching philosophy is a challenge. Taking the practical teaching of anti-diabetic drugs as an example, this paper discusses how to integrate innovative and challenging problems with the flipped classroom approach, effectively addressing deficiencies of traditional teaching models. This study is significant for cultivating pharmacy talents with innovative thinking and offers practical new ideas for reforming medicinal chemistry courses.