Abstract
The global challenge of effectively cultivating clinical thinking in medical students persists, often hindered by traditional textbooks that present knowledge in a linear sequence disconnected from the non-linear logic of clinical reasoning. This paper presents the systematic design and development of a modular “Clinical Thinking Navigation System” for a diagnostics textbook, aligning with China’s “101 Project” for educational innovation. The framework comprises seven functionally independent yet interoperable modules: Objective Orientation, Scenario Introduction, Core Knowledge, Tool Support, Visual Summarization, Integration & Expansion, and Evaluation & Reflection. This system integrates structured visual tools to make implicit reasoning explicit and trainable. A key step in the development process was a formative evaluation involving 20 medical education experts, whose feedback affirmed the system’s utility and navigational logic. Furthermore, an exploratory analysis of the system’ architecture logic using a large language model (DeepSeek) provided a complementary perspective on its coherence and scalability, characterized by three core evaluation dimensions—structural integrity, functional interoperability, and future extensibility—suggesting its potential as an ‘Educational Operating System’.This paper details the design process and theoretical foundations, arguing that the modular framework offers a replicable model for transitioning from static knowledge repositories to dynamic competency development platforms in global medical education. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12909-026-09023-y.