The low conversion rate of clinical diagnostic thinking in medical imaging is an important bottleneck in current medical education, manifested as a discontinuous connection from theory to practice for clinical medical students, specifically reflected in core issues such as the difficulty in image-pathology association, the lack of three-dimensional spatial positioning ability, and insufficient cognition of dynamic disease courses. This study breaks through the improvement ideas at the application level of traditional technologies, establishes a “three-dimensional ability matrix model”, explores how to solve the problem of low conversion rate of clinical medical students, enables students to complete the efficient transformation from theoretical courses to clinical diagnosis and treatment thinking, and achieves remarkable results in improving the quality of medical imaging education and cultivating clinical diagnostic thinking. It provides a new idea for the efficient transformation of clinical medical students’ thinking in future medical education.