Background: Holistic thinking, which is rooted in Eastern culture, is assumed to be the core of traditional Chinese medicine (TCM). Recently, such holistic thinking has been proposed to be applicable to Western medicine practices for alleviating serious side effects; however, the obscure and often ill-defined terms of TCM, such as qi, yin yang, and wuxing, pose considerable obstacles for further understanding TCM. In the present study, we explored whether and how TCM is actually related to the scientific construct of holistic thinking, to elucidate the particular cultural signature of TCM. Methods: A random sample of 101 college students majoring in TCM and 93 non-medical college students was recruited for the study. Two psychological scales—the Chinese Holistic Thinking Scale and the TCM Competence Scale were used respectively to measure the holistic thinking and participants’ ability to apply the TCM in practice. Results: We found that individuals who thought more holistically were better at applying TCM to modern medical problems. Interestingly, TCM was associated with holistic thinking in both TCM and non-medical students, suggesting that this association is intrinsic. Further exploration revealed that the association and variability facets of Eastern holistic thinking—which emphasize that the world is interconnected and ever-changing, respectively—significantly accounted for the individual differences in competence in utilizing TCM in practice. Conclusion: In short, our study provides the first empirical evidence linking TCM to the Eastern holistic thinking style, which not only deepens the understanding of TCM from a scientific perspective but also promotes dialogue between TCM and Western medicine for building safer and more effective health care systems.