IntroductionTraditional Chinese medicine (TCM) and Western medicine (WM) stem from distinct cultural and regional contexts, with the primary difference in their approaches to clinical reasoning. This study aims to investigate the cognitive preferences of TCM and WM physicians in clinical diagnosis and treatment, providing valuable insights for the advancement of TCM. MethodsWe implemented a two-phase mixed methods approach comprising questionnaires and semi-structured interviews. The Thinking Style Inventory (TSI) was used to evaluate the thinking styles of physicians through convenience sampling. Additionally, a total of six physicians (three practicing TCM and three WM) were selected by purposive sampling and open-ended responses regarding self-cognition and influencing factors were analyzed using thematic analysis. ResultsA total of 150 surveys and six interviews consistently indicated a preference among both TCM and WM physicians for Legislative, Executive, Hierarchical, Liberal, and External styles. In contrast, TCM physicians exhibited a tendency towards Legislative and Liberal styles, whereas WM physicians leaned towards Executive and Judicial styles. Thematic analysis of the interviews revealed four themes: self-understanding, thinking characteristics, influencing factors, and style changes. ConclusionOur study identified that within TCM and WM, a blend of shared characteristics and distinct individuality in thinking styles existed, exhibiting variations in the growth processes of physicians. Both TCM and WM physicians attributed the formation of their thinking styles to factors such as education, internship experience, Chinese social culture and personal disposition. Furthermore, empirical research methods emerged as effective tools for studying clinical reasoning in healthcare contexts.